I like the indoctrination theory, but I think it loses steam after TIM's and Anderson's deaths. Firstly, I think it's very possible that Anderson could be teleported closer to the console than Shepard, and I think that has just as much credit as the indoctrination theory. Same goes for TIM's sudden arrival. I think around when Shepard kills Kai Lang, must be before the fight, TIM says he's going back to the Citadel. Plus, I believe that there wouldn't be a mention of the Citadel itself shifting if it wasn't critical info to understanding what's happening. I'd put my stake into other paths being opened, allowing the other characters to arrive unexpectedly just as much as the indoctrination theory.
Anyway, as I said I do like the indoc theory, but I think it loses steam after the other guy's deaths. If TIM represents the side of Shepard that is already indoctrinated, then symbolically, it only makes sense that when Shepard destroys TIM, he breaks his hold over the indoctrination. To say that "oh, but he's still indoctrinated" just seems silly to me. Plus, after that point, if your only option do break the indoc is to choose the destroy ending, that only limits my choices even more.
Now, I'm not just left with three choices, but only one choice, which is made while Shepard is delusional. This forces the player to think that destroying machines is the only way to go. The only following outcome would be Shepard realizing that he broke the indoc. "Well, that was lucky."
I say, if you want the indoctrination theory to be true, and don't get me wrong, it's an awesome theory, it should end before the meeting with the star child. If you want a different ending, something else completely would be better.