So yeah, as neat as it might first appear, I really don't buy into the indoctrination theory. At least as far as the authors' intent goes. If that's what they really intended then they did a poor job of executing it.
The indoctrination theory is popular because it erases that final section of the game, and people are willing to forgive any plot holes in it out of a desperate desire to undo the ending. It appealed to me a lot when I finished the game, but when Casey Hudson came out with his statement and it was clear that the ending was supposed to be taken at face value, I accepted that it wasn't to be. I can understand why the holdouts still cling to it, but it's kinda sad to see so many people unwilling to accept that Bioware screwed up the endings.
I finished the game for the second time tonight, and it was actually worse this time. The final mission wasn't as dynamic as I would have hoped, but everything up until that white elevator ride was fine. After that... by the goddess, how could they have been so blind to just how shit it was?
Oh I can totally understand the appeal of that theory, but it's just a comforting lie. The most likely explanation is still the simplest.
The way I see it, at a certain point in development, they realised they weren't going to have enough time to do everything they wanted and were forced to cut back on content. I'm guessing this was about a year ago, around the same time the release date was pushed back. Naturally they had to prioritise what was most important, balanced against what work had already been done.
I'm guessing that the Prothean teamate was the first thing to go. In fact, I'd be willing to bet the original idea was to find him at the Mars dig site (there's even content still in the game that alludes to a secret Prothean facility hidden beneath the archives.) I don't know if the Aria/Omega plot was in the main game at some point or if they intentionally saved that for DLC from the get-go. Either way, after that, the main missions got priority while side missions got cut back, dropped or simplified to scan and fetch quests. then the beta leak hits are the ending which by this point is already half done is all over the net forcing them into a last minute scramble to change the ending, leaving no time for the usual peer review and multiple drafts that would normally be par for the course.
Serously, as good as the game is, look closely and the signs of a production under a the gun are all over the place. From the occasionally sloppy animations, to inexplicably useless journal and the hastily put together N7 missions. Even the crew interactions feel thin with minimal animations and only sporadic conversation trees.
I don't know if at some point they planned to "enhance" the rushed ending with new material, knowing that the plot holes will eventually be filled in, that they just figured "what the hell, only the die hard fans will even get to the end anyway" or if they genuinely thought that mess would pass muster.
This is of course 100% opinion based speculation on my part and could be *way* off the mark, but that's how I see things at the moment.
Still, to this day the biggest mystery for me remains "what the hell was the point of Diana Allers?" A character with no dicernable traits, personality, or backstory worth a fart. Your interactions with her are so widely spaced that there's no way for a player to develop any kind of attachment to her and the decision to cast as non-actor/internet "journalist" in the role is utterly baffling. I swear they must have spent more time on her in-game model than on any other facet of her involvement. Seriously, if they wanted embedded reporter then why not use Emily Wong or even al-Jilani? Even then, what's the point of having side a character if we don't get to see her reports playing when we visit the Citadel? Like everything else that should have meant something, all we get is a few meaningless points in the war assets bucket of futility.