Favorite Video Game Plot Holes

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Scorched_Cascade

Innocence proves nothing
Sep 26, 2008
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believer258 said:
Scorched_Cascade said:
EHKOS said:
Scorched_Cascade said:
Jak and Daxter: Oh man, time travel right? So it is hinted strongly that:
Jak is in fact Mar
Jak runs around picking up pieces of Mar's armour and then time travels a bit with the otsels. When he emerges from whatever it was he was doing in the past he still has the armour on.
If he is mar and he picked up Mar's old armour in the future then he must have left it at some point in the past
What's going on there?

There are also a few involving the child that is Mar's descendant in the future and what happens to him.
I can explain this one. In the game they say Mar was old. I can't remember how old but enough that he died a while back. Jak is his decendant. That little kid IS Jak. They sent him back to the first games location to protect him until he was old enough. Wether they knew he would find another time machine or just hoped to get him out of danger is still a question.
Okay I'm going to assume everyone that wants to play this game has already so without spoiler tags:

They say that Jak is his descendant but it is heavily implied by the sage/otsel characters that Jak IS Mar as well as his descendant. I.e he time travelled back built haven city and fathered a child who then fathered a child until Jak was born.

Basically they imply that he is his own ancestor. So the timeline looks like this:

-Jak is born the descendant of mar and grows up in a city at war with metal heads.
-He is captured but later saved by the resistance and future Jak.
-Child Jak then opens the temple of mar for future Jak who is too tainted to do so himself.
-Future Jak saves the city
-Child Jak is sent back in time to the past with the young green sage as his guide/mentor.
-Events of Jak+Daxter 1
-Jak, Kiera and Daxter repair the old time machine and activate it this allows the metal head leader entry into the past world from the future and his conquest begins creating a stable time loop.
-Jak is sent into the future and saves the city while picking up artifacts Mar left behind in the past
-Jak saves the world from the Dark Makers
-Jak time travels to the past with the otsel makers for unknown reason
-???
-Jak (Mar) travels back to the past to build Haven city and temples that he had already used in the future by using mako. He leaves behind his armour and other artifacts.
-Jak (Mar) fathers children one of whom is the ancestor of Jak.
-Jak is born the descendant of Mar and grows up in a city at war with metal heads
It's clever but it makes your brain hurt.

So... if Jak is his own grandfather... is that some sort of incest? This has been a point of contention amongst many fans of the old Jak games, and I don't think Naughty Dog meant for Jak to be his own ancestor, but here it is.

But why can't Damos' mother and father be someone else? Does Jak's ancestor have to be himself? Couldn't it be two random people from somewhere?
Nah it would only be incest if he displaced his natural grandfather to sleep with his grandmother (classic grandfather paradox) instead he is fathering a child with a woman when he would not otherwise have existed.

Deimos has to be descended from Jak because Deimos states that he is a descendant of Mar and is the father of Jak. As Jak is Mar he must be Deimos' ancestor.
 

baddude1337

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Jun 9, 2010
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Ordinaryundone said:
baddude1337 said:
The crazy number of inconsistencies/retcons in Halo games, such as Noble being mainly Spartan 3's even though nobody knows about them, and theres even a Spartan 2 on the team. How all the spartans seem to have regenerating shields even though chief is the only one who actually has the armor to do that, and that fact that it is Spartan 3's who are using this armor, How the Spartan's in Halo Wars have shields even though they hadn't been invented yet. That's just a small number of the many problems.
Eh, the Shields examples can really be attributed to gameplay. Sure, they could have used the stamina excuse that ODST had, but I suppose they decided to simply call a spade a spade and just have shields. Bungie's motto in these regards seems to be "the games are the canon, everything else defers to them". Plus, Noble is a special example of a Spartan squad, so its perfectly reasonable to assume they have better armor than your typical Spartan III.

As for them actually being Spartan IIIs, how is that a plothole? Its not like they go around telling everyone; in fact, its possible that nobody on Reach can tell a difference between, say, Carter and Jorge. To your average UNSC, a Spartan is a Spartan. As for having a Spartan 2 on the team, I don't really know why they bothered, but it doesn't really bother me. Jorge seemed to have a connection to Reach beyond simply being stationed there; its possible he volunteered to serve on a squad based out of it. Or maybe he just liked the team itself. There are many reasons why he'd choose to work with Spartan 3s, and we don't know enough backstory on the character to really choose one.
It's still a bit weird, seeing as the Spartan 3's weren't even known to the 2's, and seeing as all the 2's grew up with each other, he must have thought something was up as he did not know any of them.

The shield thing still doesn't make sense in terms of the lore. Gameplay I understand but it still makes no sense.
 

Arnoxthe1

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Dec 25, 2010
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WTH does Ratchet let himself be pushed around like a retard even though he has an arsenal of weapons, gadgets, nanotech, and armor that would allow him to take down a battlecruiser?

I complained about this in an earlier thread.
 

Shoggoth2588

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mireko said:
Shoggoth2588 said:
-words-
While playing Mass Effect and looking around at planets, some of them are labeled as being on reserve lists since they could one day harbor life (it's in there: those planet descriptions can get a bit wordy). I think the planet on which Dragon Age takes place is a planet that is in Council Space so therefore, The Council has made it illegal to interfere with it (which didn't stop certain people). It's strange that humans would evolve up on Earth and the Earth of DA:O/DA2 but it could be that the Humans, Dwarves and, Elves are all different versions of a singular species, with the main humanoid species living in a sort of transitional period between Darwinian extinctions.

...

I feel like a nerd for thinking this deeply into those universes...I think I need to dull myself on cartoons for a while.
 

Lieju

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Resident Evil is full of them.
-Why does Wesker hate Chris?
-What happened to the virus that brought Wesker back? They all just decided the virus that gave you superpowers without any ill effects just wasn't worth it?
-What happened to Sherry/Steve/Billy a number of characters really.
-a bunch of timeline-stuff that doesn't fit
-why is the architecture crazy and how come the player can always find the convenient emblems and cranks and stuff?
-Good timing on the part of the protagonists sometimes, like how Chris and Jill just manage to get to Spencer right when Wesker is there.
-The whole of Resident Evil Zero
 

Srs bzns

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Euhan01 said:
Pong - The story makes no effort to even exist.

Borderlands - Not so much plot holes as massive annoyance in the story.

Halo Reach - How do all the Spartans now how to use Coventent weapons/viechels that they've never seen before.

Half Life - How does a random scientist have the power to destroy everything in his path?
1. Inorite?

2. Elaborate please?

3. The Human Covenant war was going on for 20-25 years prior to the Reach Invasion.

4. I don't play HL *gasp!* But I'd say it'd be kinda dull if he spent the whole time running through labs from various monsters.
 

Ordinaryundone

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baddude1337 said:
It's still a bit weird, seeing as the Spartan 3's weren't even known to the 2's, and seeing as all the 2's grew up with each other, he must have thought something was up as he did not know any of them.

The shield thing still doesn't make sense in terms of the lore. Gameplay I understand but it still makes no sense.
Well, once again, Bungie sees the games as the foremost source of canon, with books and other EU coming in second. If a game says that a Spartan 2 was on a squad of Spartan 3s, then thats just the way it is, and it can be retroactively inferred that, obviously, not all Spartan 2s were ignorant of the Spartan 3s (which, really, makes more sense to me than having them be completely unknown). The best example, of course, is Halo: Reach itself. Its completely different than The Fall of Reach in nearly every regard, but for now is regarded as the actual events of the battle. Games overwrite EU canon-wise. Ditto with Shields on Spartan 3s and in Halo Wars, but I think that was more a retcon of gameplay necessity than a deliberate story retcon.
 

mireko

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Shoggoth2588 said:
mireko said:
Shoggoth2588 said:
-words-
-things-
Humans evolving on multiple planets isn't entirely unfeasible if the climate is similar, really. We have many examples of organisms acquiring similar traits without ever coming into contact with eachother. If the planet with Ferelden/Kirkwall/etc is a lot like Earth (and it seemed to be in DA), then humanoid life is entirely within the realm of possibility, since the human form was optimal enough for our species to survive here.[footnote]http://en.wikipedia.org/wiki/Convergent_evolution[/footnote]

You're right, this theory does lead to some interesting questions, why don't humans on Earth experience the Fade? Is the Fade somehow connected to the planet itself? Is magic related to Element Zero? Are Biotics actually SPACE MAGES?!

Are the Reapers machines infected by demons? That would explain why Harbinger (probably a hunger demon, since he sucks so much) failed where Sovereign (possibly a pride demon, he does spend a lot of time saying humans couldn't possibly understand his intentions) nearly succeeded.

EDIT: Although you're right in that it would be weird or at least unusual to have so many similar sapient races on one planet. I'm not sure about that part, let's just say a wizard did it.

EDIT EDIT: Wait.. Lyrium = Element Zero!

Now I feel like I'm a nerd.
 

Harveypot

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Shoggoth2588 said:
Elamdri said:
Ok, I know this is video game plot holes, but I'm just going to have to hijack this for a moment and turn to book/movie plot holes.

Harry Potter: Why don't they ever use the Time Turner to fix stuff?
A bigger question is, why didn't Hermione brew up more Felix Felicious (luck potion) during 6th year and summer break after? Lucky Potion would have been a really effective weapon in the fight against He-Who-Must-Not-Be-Named[sub][sub][sub]Voldemort[/sub][/sub][/sub]. Even if the trio didn't use it themselves, there was a window of opportunity during the end of year 6 when she could have left it in the Room of Requirement or something.


Read book 7.
 

Ordinaryundone

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Lieju said:
Resident Evil is full of them.

-Why does Wesker hate Chris?
Chris screwed up his plans in RE1 and in RE: Code Veronica, and on other occasions. He's been a pretty constant thorn in Wesker's side since Raccoon City.

-What happened to the virus that brought Wesker back? They all just decided the virus that gave you superpowers without any ill effects just wasn't worth it?
Well, it was untested, for one. Birkin and Wesker had an idea of what it would do, but Wesker using it on himself was its first real trial. Also, Birkin did most of the work on it, and was killed in RE2 presumably before he could make more.

-What happened to Sherry/Steve/Billy a number of characters really.
As far as the ending of RE3 goes, Sherry is in the hands of the government and Barry is either with his family in Canada or helping Chris and Jill. Steve is dead, as far as we know. No real evidence has been given to him being anything other than dead.

-a bunch of timeline-stuff that doesn't fit
Eh, its RE. This isn't exactly classical literature we are dealing with.

-why is the architecture crazy and how come the player can always find the convenient emblems and cranks and stuff?
As far as RE 1, 2, and CV to a degree, the architects who designed the buildings were certifiably insane or working on a commission to make everything as obtuse as possible for security reasons. Usually both.

-Good timing on the part of the protagonists sometimes, like how Chris and Jill just manage to get to Spencer right when Wesker is there.
Movie logic. Its not a plothole, just plot-contrived conveniences. After all, we wouldn't have gotten a cool fight scene if they'd just shown up to see a dead guy in a wheelchair.

-The whole of Resident Evil Zero
Well, I'm tempted to say "Its RE" again, but honestly, yeah. It was pretty dumb. Though I do find the idea of Rebecca going on this huge adventure and saving the day, just to show up at the Spencer Estate and have everyone treat her like dead weight to be hilarious.
 

starwarsgeek

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Lieju said:
Resident Evil is full of them.
-Why does Wesker hate Chris?

-What happened to the virus that brought Wesker back? They all just decided the virus that gave you superpowers without any ill effects just wasn't worth it?

-What happened to Sherry/Steve/Billy a number of characters really.

-a bunch of timeline-stuff that doesn't fit

-why is the architecture crazy and how come the player can always find the convenient emblems and cranks and stuff?

-Good timing on the part of the protagonists sometimes, like how Chris and Jill just manage to get to Spencer right when Wesker is there.

-The whole of Resident Evil Zero
-Chris and Jill stopped him from successfully esacping the Spencer Mansion with the BOW combat data when he defected from Umbrella. I never finished Code Veronica, but I'd assumed Chris got in the way there too.

-Wesker's virus did have ill effects. He has to take regular injections to keep the mutations under control. Also, RE5 revealed that Wesker's entire life was manipulated by Spencer, so maybe the virus was specially created for Wesker and would simply kill anyone else.

-There's a good chance that Sherry will pop up in that multiplayer spin-off they announced recently...one playable team is a US special ops group, so their ending will probably involve recruiting Leon and/or kidnapping Sherry. Besides, this isn't a plot hole, it's just something that isn't covered in the plot.

-What timeline-stuff doesn't fit? Not doubting it; it's just that some examples would be appreciated.

-It makes snooping difficult, if I remember correctly. REmake had notes from the guy who built the Spencer mansion; I seem to recall the notes mentioning that Spencer wanted the mansion like that...and the man is obsessed with cranks, apparently.

-That's not a plot hole...that's just plot. Besides, that was actually pretty crappy timing on their part, considering how that fight went.

-Never played RE0. Specific examples please?
 

Trivun

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Dec 13, 2008
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ReinofFire said:
Halo: Humanity has been able to use covenant technology for a long time apparently (thank you Halo Wars) but in all that time they still use bullets. In fact, if Spartans could use covenant technology to begin with, why didn't they use it more often (you know other than for scavenging, which by the way is not a part of war, thank you video games).
Explained, and justified with the scavenging (unlike every other shooter), in the expanded universe. Basically, there are standing orders for all Marines, ODSTs and SPARTANs to collect any and all Covenant technology they find in battle, so the ONI spooks can do whatever research necessary to replicate that technology. Bear in mind that it's perfectly reasonable to assume that we'll still be using similar weaponry and such in 500 years time as we do now, it's not a big logical leap really. In the books, however, it's stated that ONI haven't been able to replicate Covenant technology perfectly, which is why there are only certain things that are Covenant-based (particularly shield systems and artificial gravity) that humans can use. Thus the scavenging is justified and it explains how the characters can use Covenant technology, without having access to it through their usual weapon choices...
 

Lieju

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Ordinaryundone said:
Lieju said:
Resident Evil is full of them.

-Why does Wesker hate Chris?
Chris screwed up his plans in RE1 and in RE: Code Veronica, and on other occasions. He's been a pretty constant thorn in Wesker's side since Raccoon City.
Except that Wesker had planned his death and it all went to plan. Why he'd want to fake his death like that is another plot-hole, or something like it. If he expected Chris and Jill to die, why fool them into thinking he died?
Wesker already hates Chris in Code Veronica, in which he is not much more than an annoyance to him, but still it's understandable he'd hate him for that.
But then in the incident in Russia Wesker doesn't seem to care. (And his attitude towards Chris and Jill is like that in the whole Umbrella Chronicles)
-What happened to the virus that brought Wesker back? They all just decided the virus that gave you superpowers without any ill effects just wasn't worth it?
Well, it was untested, for one. Birkin and Wesker had an idea of what it would do, but Wesker using it on himself was its first real trial. Also, Birkin did most of the work on it, and was killed in RE2 presumably before he could make more.
And yet they made a big deal out of G-virus even though there was a better super-soldier-serum around. I guess it could be explained Will was just so in love with his precious he didn't consider Wesker's virus interesting enough.

-What happened to Sherry/Steve/Billy a number of characters really.
As far as the ending of RE3 goes, Sherry is in the hands of the government and Barry is either with his family in Canada or helping Chris and Jill. Steve is dead, as far as we know. No real evidence has been given to him being anything other than dead.
According to Wesker's report he took Sherry.
Those might be more of loose plot-threads than plotholes, though. They left Steve's fate kinda open, hinting that he might come back to life if they ever felt like writing him in again.

-a bunch of timeline-stuff that doesn't fit
Eh, its RE. This isn't exactly classical literature we are dealing with.
Which doesn't change the fact that they are plot-holes. Caused by the franchise consisting of that many games with different people working on different ones.

-Good timing on the part of the protagonists sometimes, like how Chris and Jill just manage to get to Spencer right when Wesker is there.
Movie logic. Its not a plothole, just plot-contrived conveniences. After all, we wouldn't have gotten a cool fight scene if they'd just shown up to see a dead guy in a wheelchair.
I still count that as a plot-hole, especially since they make an attempt at explaining it. Ada knew Wesker was coming there, Jill and Chris got a tip, most likely from Ada. But it's still a huge coincidence.

-The whole of Resident Evil Zero
Well, I'm tempted to say "Its RE" again, but honestly, yeah. It was pretty dumb. Though I do find the idea of Rebecca going on this huge adventure and saving the day, just to show up at the Spencer Estate and have everyone treat her like dead weight to be hilarious.
She just never mentions it, even when they talk about Umbrella in Re1/Remake. Not to mention the timelines don't really fit.
And Rebecca and Billy just wandering around aimlessly until they happen upon Marcus and kill him. At one point they are in Raccoon city. Just outside of Birkin's lab. Enrico is there too!

I can't say I really hate zero(and in fact there's lot of unintentional hilarity in it), but damn is it stupid.
 

Lieju

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starwarsgeek said:
-Chris and Jill stopped him from successfully esacping the Spencer Mansion with the BOW combat data when he defected from Umbrella. I never finished Code Veronica, but I'd assumed Chris got in the way there too.
No they didn't. Sergei and the Red Queen did(as we see in Umbrella Chronicles). Apart from that the whole thing with Wesker's death went according to his plan. Except maybe for Jill and Chris surviving, but if he wanted them to die, why bother faking his death in a way that required them to survive and report him dead?

starwarsgeek said:
-Wesker's virus did have ill effects. He has to take regular injections to keep the mutations under control. Also, RE5 revealed that Wesker's entire life was manipulated by Spencer, so maybe the virus was specially created for Wesker and would simply kill anyone else.
Birkin tested the virus on animals and reported decent success http://residentevil.wikia.com/Virus_Memo
And even if he had to take injections, it still was a better super-soldier serum the other viruses were.

starwarsgeek said:
-What timeline-stuff doesn't fit? Not doubting it; it's just that some examples would be appreciated.
Like, for how long was John (The one Ada dated) the head researcher at Arklay? I recall trying to find that out some time ago for a fanfic I was writing and different memos and raports giving different dates for when he came from Chicago.
Or Birkin mentioning Alexia in a memo and talking like she was alive, though at that time they thought she had died. Well, maybe Will was just insane.

starwarsgeek said:
-It makes snooping difficult, if I remember correctly. REmake had notes from the guy who built the Spencer mansion; I seem to recall the notes mentioning that Spencer wanted the mansion like that...and the man is obsessed with cranks, apparently.
But you could still find all the emblems and whatnot.
But that all can be filed under "stuff for the convenience of gameplay"

starwarsgeek said:
-Never played RE0. Specific examples please?
Rebecca has this whole adventure before the events in the mansion, fighting tyrants, zombie-monkeys and giant bats in an another mansion before that. And yet she never mentions this to anyone and is defenseless against one hunter, despite killing dozens of them just few hours ago.
And Rebecca and Billy wander to a random factory to kill Marcus who is there for some reason. They are in Raccoon city at one point (Enrico too)and somehow make their way back in time.

Not to mention the whole retconning the first virus-leak in the Arklay-lab raises more questions, as in, if Marcus was behind it, why are there no zombie monkeys or leeches around, and why did he choose such an inefficient method for his revenge anyway, given that it was Birkin and Wesker he was angry at, and neither was at that lab.
 

Lieju

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mireko said:
Humans evolving on multiple planets isn't entirely unfeasible if the climate is similar, really. We have many examples of organisms acquiring similar traits without ever coming into contact with eachother. If the planet with Ferelden/Kirkwall/etc is a lot like Earth (and it seemed to be in DA), then humanoid life is entirely within the realm of possibility, since the human form was optimal enough for our species to survive here.[footnote]http://en.wikipedia.org/wiki/Convergent_evolution[/footnote]
Not really. Even if the world is very similar climate-vice, it would take quite a lot of coincidences to end up with a similar humanoid structure. It isn't even particularly good design choice and is a result of an accident more than anything. Humans are the only ones on this planet with this structure, so it isn't that advantageous. It works, sure, but it isn't that great a design, (especially in humans where it developed from a non-erect form so our muscles and organs are all stupidly placed). So why would evolution end up with something similar in a totally different world?
Some similarities, like the ability to hold things with hands or whatever passes for them would be present, but the whole humanoid appearance?

In the case of convergent evolution, it can end up with similar solutions in different evolutionary branches, but because the structure it starts with is similar enough the result is similar. As in, both fish and dolphins have evolved similar form, but both share an ancestor that had bilateral symmetry, and eyes, and a skeleton and whatnot so they do too.

If we would have another planet with their life evolving completely separate from ours, there's a long chain of mutations and chance playing part.

Convergent evolution would happen.
Creatures adapted to the life in water would take similar forms than what we have because they are advantageous in moving in such an element. Different creatures would develope eyes, because detecting light is advantageous and there are several ways to do it. Animals would develope ways to fly, and ways to dig and shield themselves from the elements, and same kinds of solutions would exist, but there's no particular reason to develope humanoid shape.

It is a result of a chain of unlikely coincidences, and not that great a design, and even on our planet, only one evolutionary branch went for it.
 

carpenter20m

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Has anyone thought that the Earth of Mass Effect is our Earth?

An Earth that has played games of the Dragon Age franchise?

My guess: Dragon Age is huge, the best game ever in the future (ME's present). Big VR installations take you to Thedas, where you wield your sword against the darkspawn.

So, the Ogre is nothing but a reference to people's favorite game.
 

Zechnophobe

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wouldyoukindly99 said:
Not really what you would call "Favorite" since it kinda spoils the story but, Bioshock:

So Fontaine sends Jack to the surface as a baby right? What happens when he gets to dry land and exits the sub? How did he survive alone, as an infant no less, on the surface? We learn that his memories of a family are fake, so he probably didn't live with anyone on the surface, how did he make it as a baby all the way to able-to-buy-a-plane-ticket-for-myself adulthood?

Also, how did Fontaine know where to send the package? Did he have someone tailing Jack his whole life?
Er, that's completely answerable actually.
They have a fair bit of stuff in there talking about how he aged much MUCH faster than normal. Even if he was just a boy he'd have still been able to make it. As for getting the package etc etc, it isn't really a hole, as that would imply a contradiction or impossibility. There are plenty of ways it could happen, they just didn't tell us in the story.
 

Zechnophobe

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Anyhow, my contribution comes from... Dragon Age 2.

At the end of Act 2...

Isabella will return with the 'relic' right before you confront the Arishok. She gives it to him. You can then choose to not duel, and instead kill every qunari in the Room.

Later on Isabella gets in trouble with Castillon for not having the Relic.

But... where did it go? You KILLED all those Qunari right? Couldn't you have looted it off the corpse of whoever had it? It basically just disappears, and no explanation of where it went is ever given.
 

Ordinaryundone

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Lieju said:
Except that Wesker had planned his death and it all went to plan. Why he'd want to fake his death like that is another plot-hole, or something like it. If he expected Chris and Jill to die, why fool them into thinking he died?
Wesker already hates Chris in Code Veronica, in which he is not much more than an annoyance to him, but still it's understandable he'd hate him for that.
But then in the incident in Russia Wesker doesn't seem to care. (And his attitude towards Chris and Jill is like that in the whole Umbrella Chronicles)
Well, Wesker doesn't seem to care because he's a smug bastard. Even if Chris did seriously screw things up for him, Wesker would never show it. Hell, even through RE5 where Chris is throwing a wrench into nearly all of Wesker's machinations, he doesn't even get angry until near the very end when literally everything is over.

And I'm pretty sure Wesker didn't PLAN his death in RE1, though it's been a while since I played it. From what I understood, his original plan was just to get the data and sell it, which Chris and Jill screwed up pretty royally. The rebirth virus was just a contingency plan in case things went awry. I'm pretty sure Wesker wasn't faking his mauling from the Tyrant; if anything, that was probably a genuine miscalculation on his part. Honestly, like I said, there was no way of really knowing what that virus would do. The only thing he seems sure of in the Wesker Report is that it would bring him back to life; I think superpowers were a happy coincidence. Wesker would be too smart to get himself killed on purpose over something that might not work.

And yet they made a big deal out of G-virus even though there was a better super-soldier-serum around. I guess it could be explained Will was just so in love with his precious he didn't consider Wesker's virus interesting enough.
Well, Birkin never got a chance to really see the effect IIRC. Wesker went into hiding after RE1, and RE2 happened shortly after. And like you said, Birkin was in love with G-Virus. It was his life's work, and he considered it superior to everything, even T-Veronica. Guy had an ego the size of a truck, so its fairly believable he'd snub the results of rebirth even if they were presented to him.

According to Wesker's report he took Sherry.
Those might be more of loose plot-threads than plotholes, though. They left Steve's fate kinda open, hinting that he might come back to life if they ever felt like writing him in again.
Didn't Wesker just say he recovered Steve's body? I mean, the virus is still in him but I doubt Wesker would have had any interest in reviving Steve. He probably just wanted the T-Veronica sample. As for Sherry, who knows? That story has long since stopped being relevant as G-Virus never came up again. I actually like the idea of her being safe with the government better, as it gives a more closed reason as to why she never shows back up.

Which doesn't change the fact that they are plot-holes. Caused by the franchise consisting of that many games with different people working on different ones.
Timeline inconsistencies don't necessarily equal plot-holes. In movies it happens all the time: The hero has only a minute to disarm a bomb but the scene takes longer. No one considers it a plothole, its simply done for drama. Likewise, not all the games fit absolutely perfectly together, but thats done more for the sake of storytelling than anything.

I still count that as a plot-hole, especially since they make an attempt at explaining it. Ada knew Wesker was coming there, Jill and Chris got a tip, most likely from Ada. But it's still a huge coincidence.
I doubt its from Ada, as she has no idea (as far as we know) who Chris or Jill are. My guess: Spencer sent it. He knew Wesker was coming to visit, and he knew it probably wasn't a social call, so who better to call for help than Wesker's archrival? If Chris had made it just a few minutes earlier its very possible Wesker would have tried to kill him before Spencer, and it might have saved his life. No one else would rank that high on Wesker's kill on sight chart.

She just never mentions it, even when they talk about Umbrella in Re1/Remake. Not to mention the timelines don't really fit.
And Rebecca and Billy just wandering around aimlessly until they happen upon Marcus and kill him. At one point they are in Raccoon city. Just outside of Birkin's lab. Enrico is there too!

I can't say I really hate zero(and in fact there's lot of unintentional hilarity in it), but damn is it stupid.
To be fair, no one really asks her where she has been, so maybe she'd feel rude bringing it up? After all, they did have bigger problems at the moment, and she wouldn't want to let anyone know about Billy. And yeah, the story is pretty aimless, but I kinda got that vibe from most of the early RE games. 1 and 3, especially. Though nearly all of them have heroes who sort of just wander about until the run into the story. Its probably why 4 and 5 feel so different.