At this point, Bioware would be crazy to not just pretend the "indoctrination" theory was the plan from the beginning, because at least theres something in that interpretation to think about.
In my eyes (and perhaps I'm also being indoctrinated) most of the "facts" people are using to back up the theory are signs of a rushed product. Thats all it looks like to me. Bioware claiming this was their original intention, be it the truth or otherwise, would allow them time to step away and come up with something a little more focused and polished- certainly a wise decision, though its clear that they'll never be able to all expectation.
A couple of loose thoughts to add on to the discussion over the ending:
- How cool would it have been if it turned out Shepard was actually a synthetic? This was a silly pet theory of mine, not one I expected to happen, but one that seemed appropriate given the nature of the game's ending. Think about it: TIM can't afford the loss of someone so vital to mankind's position, so he creates a synthetic version of Shepard that looks and acts identically to the original, so much so so that it even has itself fooled. Plus its more believable than them simply bringing charred remains (remember his brain, the core of one's personality, must have been completely destroyed) back to life.
This would give the ending scene with TIM a powerful twist ("You aren't even the real Shepard- I created you in order to further my own interests") and add a lot of weight to the game's attempt at making you contemplate the nature of organic and synthetic life. Also, it would be neat to find out the savior of organic life was actually a synthetic meant to replicate organic life- I'm sure the Reapers would get a kick out of that.
-Speaking of the Reapers, I'm fine with them being such big fans of Gurren Lagann, but it would have been nice if they did a little more convincing on their end (especially in the face of you negotiating a peace with synthetics...). Picture the same scene with the Catalyst, though this time around Shepard is basically lectured on how synthetic life has no limitations, that it has already seen and conquered the universe, and that organic life is/was only a stepping stone on the path to creating synthetic life, nothing more. Organics are kept around as a novelty, galaxies tended to and "weeded" like gardens.
Killing life to save life? Okay, sure, I can deal with that. I just imagine an AI of that magnitude would have a lot of time to come up with a really compelling argument to the first pathetic organic it meets. Maybe just throw out some statistics to back up their theory ("This is what has happened an untold billion number of times before your own cycle", etc) and make it seem like they really are doing organic life a service, since thats apparently how they see it.
(note: I fully expect, like Gurren Lagann, for their to be a "something" beyond the Reapers (as the Anti-Spiral were to the Spiral King) that will become much more interested in the galaxy in light of the Reaper's failure)
-Aside from the poor delivery, I think the ending leaves the Mass Effect universe in a very interesting place, and am fascinated by what will come out of the state Shepard has left the galaxy in now that they're pretty much stuck wherever they were at the time of SPACE MAGIC. I never needed a happy ending, just a satisfying one, so I'm at least interested in what they decide to do next.
