I wanted to create a new thread where people won't have to post a spoiler warning at the top of every post.
A bunch of people have been fairly unhappy with the ending but recently a theory has come together that seems to explain most of the confusion behind the game's ending.
As Li-on pointed out, the final choice of the game was likely a final appeal by the Reapers to convert Shepherd to their side. Option 1: Control the Reapers (yeah right) Option 2: Synthesize with the Reapers (like the Protheans) or Option 3: Destroy the Reapers
The indoctrination theory wraps this up fairly well by stating most of the events that happen after Shepherd is hit by Harbinger's red beam are in fact an inner conflict in Shepherd's mind. This explains why Anderson and Illusive Man are conveniently waiting for him on the Citadel and the Gray Sweatshirt Kid (who was likely a hallucination the whole time) presents himself as a Godlike being, the Catalyst, and in control of the Reapers. All 3 games have focused very closely on indoctrination with Saren, Illusive Man, Harbinger, Rachni Queen, the Geth etc. There's even a codec that warns specifically about the dangers of indoctrination and talks about symptoms that Shepherd displays in this game...
The video goes into even more depth but I think most of the arguments that I've read trying to contradict the indoctrination theory fail to answer the questions presented at the end of the youtube video that indoctrination theory resolves. While I don't think the ending completely resolves the game, I'm at least happy that the game now makes sense. For me it's like the ending of BSG or Brazil: the reality of your situation is grim but there's beauty in accepting defeat and giving up on the hope of a brighter future.
Anyway, what opinions does everyone else have on the whole indoctrination theory thing?