This theory actually makes the ending decent. If this is not what bioware intended to go with the story line, they should watch and capitalize off this.
Heard they aren't gonna change it, but just add more to it. which is fine with me. I just would like to know more about the story of my squadmates after my decision.
I can't see how it actually makes the ending decent. I think a lot of people aren't taking into consideration the fact that the indoctrination theory means that Shepard is lying on the ground, dead... or best case scenario, almost dead without finishing the fight, or even knowing how it ended.
Think about it. If the indoctrination theory holds true, then Shepard is unconscious after being hit while running towards the beam of light. That means that the only ending in which he actually regains consciousness would be the 'best' ending because everything that happens after that point is only happening within his mind. Draw that to it's natural conclusion. He never actually made it onto the citadel, never actually had the confrontation with TIM, Anderson and Star-boy... none of that happened in reality. And BTW, those confusing video clips about what happens to different squad mates... all in Shepard's mind too. IF you get the 'takes a breath ending' it happens after the clips of what supposedly happens to your squad mates.
So according to the indoctrination theory, Shepard gets killed (or best case, mortally wounded) in the final hour of the conflict that this whole series has been leading up to, without ever seeing IF it ends or how. Unless somebody is going to start saying something like; Oh yeah, BTW everything that happens in Shepard's indoctrinated mind while he's unconscious actually happens in reality too. I'm not buying that for a minute.
MPO, we could just call it ME 3 indoctrination theory: Don't Finish The Fight.