I initially dismissed this theory as wishful thinking, but I've seen the light and have been converted. Hallelujah, amen! I'm actually going to start a second playthrough with the sole intent of looking for all the little clues throughout the game. The indoctrination theory is, at this point, the only logical solution to this fiasco.
Apologies if I repeat anything. 100+ pages is a lot to read through.
* The Normandy could have been compromised when it was infected with the Reaper virus in ME2. EDI locked it down for the rest of that game, but it could have infected various subsystems to facilitate indoctrination, even if Shepard managed to blow up the Collectors. A Reaper contingency plan that could float around undetected.
* Vega seems to be a voice of reason, if only because he's so new to the whole thing. "It's like the Citadel was made to keep people calm." I actually agree with some comments that, since its a critical Reaper device, it could be engineered to promote a sense of tranquility and submission. Maybe, apart from genetic meddling, that's why the Keepers are so docile.
* The Derelict Reaper mission in ME2 is potential foreshadowing. The indoctrinated crew comments on seeing things that aren't there, whether it's structural (Anderson: "The walls seem like they're shifting, moving!") or just related to objects (the kid). It even extends to memories and beliefs. Basically, indoctrination messes with every sense of perception you have.
* The Catalyst is just an unreliable narrator. It makes no negative comments about Control or Synthesis - even if both options present potential drawbacks - and lays the guilt on thick for Destroy. It's a fairly big deal that it's the only one the Reaper AI doesn't. want. you. to. pick.
* Saren was meant to be a sympathetic villain, and your situation is basically meant to mirror his in a form of tragic poetry. The indoctrination throughout the game is meant to break down Shepard's confidence and hope -- pushing the player closer toward Saren's urge to compromise and work with them in order to avoid eradication. Or to the Illusive Man, who blindly wants to control them even though that's a really bad idea.
* The final battle, then, is effectively against Harbinger itself. It's just a battle where the player's knowledge of indoctrination is tested after three games of warnings. You just get to imagine that Shepard finishes the fight after you wake back up. Which sucks, but.... it's better than the alternatives.