If the Catalyst's entire justification for the Reapers and destroying advanced civilizations was that synthetics will eventually wipe out ALL life, shouldn't have the Geth's actions have proven it wrong, thus giving it ample reason to stop this nonsense? They could have destroyed the Quarians as they retreated centuries ago. Then, depending on how things played out in your game, they could have again wiped them out after Legion sacrificed itself to give them all the Reaper upgrades. In fact, the only time when the Geth seemed completely intent on wiping organic life is when they were controlled by the Reapers!
So, the Catalyst controls the Citadel. If that's the case, then why was whatever the Protheans did to the Keepers to stop them from being able to turn it into a mass relay for the Reapers work? Couldn't have the Catalyst simply have undone it?
The Human Reaper that the Collector's were building in ME2 never really made any sense to me, until we learned the true nature of the Reapers. Creating a Reaper that looks like the destroyed civilization keeps in line with the idea of "preserving" it. But if that's the case, why do the other Reapers all kind of look like squids? Shouldn't there be all different kinds, to represent the different races they have helped "transcend" over the years? Why weren't they also building Reapers based on the other advanced races of this cycle?
What is it about Shepard reaching the Catalyst that makes it think its plan no longer works? I don't really see how one organic being getting there changes anything. Shouldn't it have been like, "Hey, man, sorry, but I gotta wipe you out...so that you don't build other organics that will wipe everything out...or something like that." And if had the ability to somehow combine synthetic and organic life...why the hell didn't it just do that before, instead of terrorizing the galaxy for millions of years?
What dumbass "advanced" race let the Catalyst set this in motion? I mean, I am assuming that Bioware isn't gonna say that the AI just magically appeared or is "God." So, someone invented this AI and asked it to solve the problem of synthetic life. Don't get me started on the stupidity of asking a synthetic life form to solve the problem of synthetic life forms.
This doesn't have to do with the ending, but it's a question that ME3 ends up raising. If the Protheans looks like Javik, then what were those statues on Ilos of? Maybe the Prothean "gods," ie whatever advanced race came before them? If so, at least that would explain why the Reapers look like squids. Well, doesn't explain why they all look squids...