But there really aren't obvious hints in the game. At no point is it the most apparent explanation for what's going on. We have the dream trees appearing around the conduid, but the whole sequence surrounding that is so sketchily made that you can't say that anything there points to anything. In fact that goes for the whole game: a lot of it is so sketchily made in at least some aspect that a far closer explanation for everything odd is that it's just odd.
That's exactly the problem - there are aspects of the game that strongly suggest indoctrination, but they're all ambiguous to varying degrees. And game design and production being what it is, it's just as easy to dismiss them as weird videogame shit than to view them as evidence of a greater sub-plot. As we all know, games aren't movies. In a movie, every shot is carefully selected. Fuck-ups still happen, but it makes much more sense to view glaring inconsistencies as directorial choices than it does with a game.
Many of the indoctrination theory arguments can be dismissed due to videogaming conventions. Shepard has infinite ammo...because it's a videogame. Shepard can't roll away from Harbinger's beam...because it's a videogame. Joker left the battle and somehow saved the squad...because it's a videogame. Etc, etc. But just because these can be explained by videogame conventions, it doesn't follow that all the supposed evidence can be written off so easily. The dream trees appearing around the beam are hard to explain. The fact that Shepard can only survive if the Destroy ending is picked when Synthesis is the hardest to unlock, and is generally pushed as the 'correct' ending - and when Destroy is specifically supposed to kill him - is even harder to explain. And whether it was intentional or not, Shepard does appear to exhibit all the classic signs of slow exposure to indoctrination during the game.
After watching the indoctrination theory video, I was convinced that Bioware had set the whole thing up; because as crazy as the theory is (Bioware released an unfinished game on purpose with a plan to deliver the real ending as DLC) it felt significantly more plausible to me than a literal interpretation of the ending. Bioware's writers are far from perfect, but I honestly can't believe that even they would come up with the ending as rote, for all the reasons we've been discussing. It's not just bad, it's inexplicable, and goes against all the themes thusfar presented in the game (diversity, peace, no meaningful difference between synthetics and organics). Yet synthesis perfectly echos Saren's goals under indoctrination. And control perfectly echos the goals of the Illusive Man under indoctrination.
At this point, I lean towards the idea that Bioware initially created the current ending as nothing more than an indoctrination sequence, but due to time restrictions cut off the twist and ended up converting the dream into the 'real' ending - either with a plan to revise it via an epilogue that fell through until the complaints rolled in; or simply hoping that people would be satisfied with it despite the fact that it makes no sense. That would explain why the indoc theory fits so well, but also why the epilogue DLC wasn't forthcoming according to a sensible production plan to finish the ending.
I still haven't really heard evidence to suggest that indoc theory couldn't have been written in from the start of ME3's production and then cut or put on hold, with remnants still remaining in the game. And the only explanation for the inconsistencies and general awfulness of the ending is 'bad writing' - nothing that couches the ending in the context of the game and has it make sense on a narrative level.
For these reasons, I expect the epilogue DLC to be in line with indoctrination theory. I think it's a plot thread that existed in the game which was dropped after being worked into several scenes, that these scenes were spotted by players, and that the idea will be resurrected by Bioware for the DLC. I don't think an indoctrination epilogue will prove beyond all doubt that Bioware has been planning this from the get go, because they clearly didn't have a big stunt planned to hold back the real ending and release it later.
Something certainly went very wrong with the production of the end of the game, but what that something was, and how much better things would be if Bioware had sufficient time to finish, is anyone's guess.
