Shamus, I have to say that was one of the worst critiques I've read, on anything gaming related. Ever.
Most of your issues were legitimately explained in ME2, or are just plain wrong\ill thought out.
"Mass Effect 2 opens with the death of Commander Shepard. This is an inept way to begin a story."
First off, Shepard dying was obviously a way to reset the character, in addition to tying him to Cereberus. Without that, there would be no reason he'd work with them, but now he sort of owes them. It's a perfectly fine mechanic, and I'm pretty sure Kratos died in GoW 2, and it worked fine as well (sure, him dying in nearly every game gets a bit old).
"In the previous Mass Effect, Cerberus was a clueless, fumbling terrorist organization."
What in the world gave you that idea? They were able to take out an Alliance rear Admiral! They had their hands in nearly everything Shepard encountered, from the rachni, to the husks, to the Thorian and its Creepers. They were evil enough to sacrifice human lives to achieve whatever ends they had in mind. They didn't care about humans, they cared about where humanity ended up. I at no point saw them as "inept".
"They build a ship better than the previous Normandy, which was the most advanced ship in the galaxy."
If by "better" you mean "more comfortable", sure. It's not like they created a vastly superior ship, but in two years time made a redesigned ship.
"They claim that all of the Cerberus agents you encountered in the previous game were "rogue elements," but that doesn't make any sense because this new Cerberus is both too competent and too focused to have countless rogue cells wasting resources and working counter to Cerberus goals."
Or that's the Illusive Man lying to Shepard
:gasp:: I know, startling to think about), so that Cerberus doesn't come off as evil and Shepard will work with them.
"They know more about the Collectors (the bad guys) than all other races combined."
Which at the start of ME2 amounted to next to nothing.
"The Alliance refuses to help you, because you're working for Cerberus. And you have to work for Cerberus because the Alliance won't help you. Even your own dialog tree works against you."
Either that or it is because they brought you back from the freakin' dead.
"Then we get to the "trap." The Collectors set aside their important collecting work to set an obvious trap for one guy."
Yeah, the guy responsible for taking down a Reaper. The one they perceive as the closest thing to a threat.
"Their trap depends on Shepard being an idiot and personally boarding their vessel, instead of blasting the ship at a distance or sending in a team of subordinates."
Yes, because Shepard ALWAYS sends his subordinates to do the job. It's not like he's the squad leader and goes out on every mission or anything like that. Not to mention they knew Shepard was looking for information on them, and he didn't know the Collectors only had one ship and one big base. Blowing up that ship from a distance would only make them lose their chance to find the Collector base.
"Then Shepard does fall for it, and their plan fails anyway. They have the drop on him, the home field advantage, superior numbers, a more advanced ship, the guidance of a Reaper, and they still can't kill him, thus establishing themselves as bumbling fools."
Or they just underestimated him? Given that they had all of these advantages, why would they expect that he'd be able to fight his way out, or that he'd have brought an AI on board which basically saved his ass?
"Worse, they didn't even need to beat him in a gunfight. They could just have flown off with him and left the Normandy behind."
Except that the ship needed time to power up, remember?
"What was he afraid of that he was willing to risk everything?
That if it looked like Shepard knew, they'd power up the ship before Shepard had a chance to get to the data module. It might be a huge risk, but I could sorta see how someone could think he'd have a better chance of completing all mission objectives that way.
". The game never really gave you a goal except "Go on the ship. Okay, now fight your way back out." Why didn't he blow up the supposedly helpless ship?"
Except for the whole part of "find information". Hard to do that if you blow up the ship. Not to mention they had no idea how the ship worked, or if it was even functioning. The important thing was finding a way to the collector base.
"Why didn't he have explosives for wrecking the ship once he was inside? What was his goal?"
If EDI went into the systems, found that all of the collectors in the ship were actually dead, they probably would have tried to take it apart and learn more from it.
"Remember that one of the great challenges that Shepard is facing is that nobody believes in the Reapers. So here we have one, all of a sudden. Then Shepard boards it and ... blows it up?"
The council already didn't believe that the ship was a Reaper, only that it was a Geth ship. A dead Reaper would not have been proof, and if I recall (I could be misremembering) they needed to do something to escape that had the effect of blowing it up. Oh, but you are right, the better thing to do was to have the Citadel send a team to a ship that would slowly turn them into mindless zombie husks while trying to verify what the ship actually was.
"How about taking a video and putting it up on YouTube, Shepard?"
Yes. I can see that now. "Wow, Shepard. That's the inside of a ship. This must mean the ship was once a sentient creature bent on destroying all life in the galaxy once every dozen million years or so, and there's certainly hundreds more on their way now!" Leap in logic, anyone?
"Remember the whole point of getting the IFF is to go through the Omega-4 relay (Which no-on has ever survived!) and kill the Collectors. But, if our only goal is to kill them, then why go to all this trouble to pass through the dangerous relay and fight them on their home turf? Why not just sit on this side of the relay and spawn-camp them? Maybe put down some mines for good measure."
The relays are linked. Unless the Collectors had business in that cluster, their ship would not appear at the Omega-4 relay. Even if they killed the ship, there would be nothing stopping them from building another, and again, Shepard didn't even know how many ships they had.
"In fact, why not just blow up the relay? When the game came out, people suggested that Mass Relays were perhaps invincible. But then the Mass Effect 2 DLC came out and gave us a mission where you have to blow up a relay, retroactively making the entire plot of Mass Effect 2 a needless risk and a pointless waste of time."
Yes, why not spend months on a project to throw a giant asteroid into the relay, which would then explode and kill everyone in the entire system, and strand anyone else in other pockets in that cluster. I'm sure there wouldn't be any problems with that.
"At the end you're given a false binary choice: Blow up the collector base, or give it to Cerberus. If you blow up the base, then you really did come here for nothing."
Yep, all for nothing, except taking out a dangerous pawn of the Reapers and stopping them from creating a new Reaper. Or as you call it: "nothing".
"You're standing on a pile of technology, intel, and proof that the Reapers exist, but apparently it's "too dangerous", because ... I guess everyone else in the galaxy is too stupid to be trusted with it?"
True, it's not like it is possible there could be any indoctrination going on inside the ship, or that Cerberus is the closest faction that would lay claim to it before anyone else would?
"The idea is that Cerberus is so strong they can take the base from you. But if they're powerful enough to overcome Shepard, who captains the most advanced ship in the galaxy, then they didn't need him in the first place."
What is Shepard going to do, sit there and babysit it? The Normandy was damaged, who is to say it would be certain Shepard could hold out? That sort of technology could actually be too dangerous, and would upset the power balance, which could cause a war right before the Reapers arrive.
I really doubt you put any thought into this. More likely you saw a something that didn't make sense to you at the time and said "it must be a plot hole" then left it at that.