After reading the thread, it has become clear (to me at least) what the actual problem with ME2 is. There was no CLEAR reason for the direction that ME2's main story arc took. Nothing so solid that it becomes irrefutable to all but the most hard headed fans. (I may actually fall in the category)
Now, those who find a reason use some very good arguments but also a lot of guesswork and conjecture to make the story fit into the trilogy. Are they wrong, not really.
Those who find no reason also make very good arguments but again, there is a lot of guesswork and conjecture to show how it does not fit into the trilogy. And again, they are not really wrong.
First, it was unclear in how the actual main plot truly has any impact on the main arc of the trilogy. Had Shepard actually found something of real use in the CB then the plot would have some trilogy based explanation, but nothing was found except the human embryo Reaper was a silly boss fight. What Cerberus might or might not find is irrelevant as Shepard does not have it. He is, after all, the protagonist. If it was clear, if something had been found, then there would still be sniping but not full on arguments. And those arguments would mainly be limited to the choices made, not why were the choices even there.
Second, the total revamp of the game broke almost all continuity between ME1 and ME2. Anyone who says they are the same game, just different chapters, is fooling themselves. I am NOT saying that one game is better than the other, I am saying they are in fact two separate games where the only link between the two are names. Almost the entire ME universe was changed between the games and only weak explanations (in game/codex) were given to explain it. The discontinuity does cause confusion and or irritation in a great many players. To make matters worse, it appears ME3 is relying on books to actually dictate some of our choices (though I may be wrong here). This only muddles the issue of continuity even more and is a slap in the face from the writers in respect to the choices we, the players, made in game.
Third, instead of being able to pull back the ME1 squad, maintaining some continuity, an almost entirely new group of (what seems to be) throw away characters were created. In ME1, the entire squad had plot armor. There is no reason why they could not have been in ME2 with the same armor and CONTINUED to work with Shepard. Yes, Wrex is working on Tuchanka, but another could be doing it at well by standing as a proxy for Wrex. The VS and Liara would have not needed character assassination to keep them safe.
These changes upset/irritated many many fans and in the end, ME2 failed to explain just why. It is that lack of clear explanation that is at the root of all arguments. Unfortunately, there is nothing we, as the fans, can do about the discontinuity. We are forced to accept it and hope that ME3 is actually able to pull the previous two games together into something that fits. The fans did not create this mess, the writers did, all we can do is wait and see.
Rambling off.