ME3 plotholes huh? Well, apart from the earth missions at the end the plot itself is actually quite consistent.
There's a few points though:
1: If you destroyed the collector base in ME2, the semi in-tact reaper will still be in TIM's base. How? We see everything get vaporized in ME2's destroy ending. The base, ships thousands of miles away, everything. Yet TIM managed to salvage a mostly in-tact human reaper? It was at the heart of the explosion.
2: Why didn't the reapers attack the citadel first, and then the planets? The whole point of ME1 was that the reapers' tactic was to control the citadel, thus controlling all the relays, cutting all planets off from each other. There was no reason for them to suddenly change tactic. Heck, there were reasons against changing tactics. For one, keeping communications and travel between planets accessible.
3: When the reapers do take the citadel and control the relays, they close them all for travel...except the sol relay. For no reason whatsoever. Heck, they bring the citadel to that place for no reason whatsoever as well. It's one of the worst places to bring the citadel, even.
4: Guns magically appearing on characters in cutscenes, when they weren't even equipped with those weapons.
5: The conduit in ME3. That beam thing that takes you up. That is not the conduit. It doesn't look like the conduit from ME1 at all. You can say it's a 'different' conduit, but come on, really? They even specifically named it the same, and it provides the same basic function of 'teleporting' you directly to the council area. And if the beam thing isn't the same conduit indeed...why not use the conduit on Ilos to get into the citadel? (this one's particularly insulting to the intelligence of the players imo. As if we'd forget the entire focus of your mission: To find out what the conduit is and to then find it.)
6: Heavy weapons have no effect on reapers in the previous games. Yet a cain in ME3 can take down a reaper with a GtA gun attached to it? They even took away heavy weapons as a standard weapon slot like you had in ME2.
7: The beam is used to transport humans to the citadel. What happened to their previous method of transporting humans? They don't use seeker swarms, don't appear to have shuttles...any means to transport humans really. So how did they do it before? (this one's a plot hole in the sense that something wasn't explained in the plot at all, and then something else took it's place.)
8: If the beam can penetrate the hull of the citadel (you see the beam hitting the citadel while it's closed off) why not just fly into the beam with a shuttle? Or if the citadel was open at the bottom, why not just fly through that hole?
And after this we pretty much get to the final run to the beam and the ending, and I'm not doing that part.
Oh, one more btw. A minor one that didn't really bother me. When the entire fleet arrives in the sol system, they arrive near Jupiter. From there they go at 'normal' speeds, not FTL speeds. (no FTL blur around vehicles, no red/blue-shifting, etc.) So what, did the entire fleet just slowly fly to earth over the next hour or two while they were in such a hurry? Or did they jump back into FTL speeds again? It's not explained at all.
EDIT:
Oh, actually one more I remembered. >.> The space battle between the fleet and the reapers... The space ships fire their largest guns at the reapers. One of those slugs hitting earth can disrupt an entire eco system in that area. They're firing hundreds of those at the reapers, and not nearly all of them hit. Not to mention all the debris from the space ships and few destroyed reapers also falling back to earth. Earth should have been a wasteland after the battle, yet in the extended cut (which is canon now) we see them rebuilding a planet that's still fairly in-tact.
