I'd buy into the Indoctrination Theory if there wasn't a plothole so big you could drive a Mack Truck through it.
The Illusive Man's role.
See, according the theory, TIM represents the indoctrinated part of the mind, except there's one fatal flaw: it's the Illusive Man. The same man Shepard despises. The same man Shepard doesn't trust in the slightest. Arguably, outside of the Reapers, Shepard's greatest enemy (more so than Saren, even). They talk about in the codex how Indoctrination turns enemy into friend and friends into enemy. Yet in this scenario, the Reaper Indoctrination doesn't do that. It turns enemy into... well, enemy. Why would the Reaper Indoctrination allow the Illusive Man to represent the Indoctrinated aspect of Shepard's mind? It makes it much easier to resist someone you don't trust and you despise. If the Reapers were trying to trick Shepard into betraying himself and falling under Indoctrination, why not use Anderson? Take a father figure that Shepard trusts, and turn him against him. Makes it much easier to control Shepard when you present him with his friends turning against him. And considering the fact that at no point does Shepard fall in line with TIM's line of thinking and EASILY resists him (either verbally or physically after he initially shoots Anderson) shows that either the Reapers are pants-on-head stupid in terms of Indoctrination or that the scene you're watching play out is real.
There's also the fact that when present with the choices, the visual representation of the "control" option is TIM. Now, once again, why are the Reapers allowing an image of Shepard's greatest enemy to represent the choice they want him most to fall in line with? Why would Shepard ever go with something the Illusive Man wanted to do?
There's also another big plothole: no one is able to recover from Indoctrination. Everyone that's fallen under it has never been able to fully break it. They can resist, temporarily, and it's why guys like TIM and Saren chose suicide. It's why Matriarch Benezia temporarily broke it only to immediately fall back under it's control. The closest you can come is the Rachni Queen. And considering that they speak telepathically via music, I assume that's what makes them somewhat immune to Indoctrination.
Also, the Mass Relays blowing up really didn't bother me because they were created by the Reapers, and destroying them was supposed to be symbolic of the galaxy now forging it's own future rather than using the future laid out for them by the Reapers.
See, the problem I have with the ending is so much of it has to be extrapolated rather than shown. I don't mind what I saw, I just hate what I didn't see.
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TheRock ~ Slow dramatic zoom-pan. Doesn't phase the hooded man.
"You have issues." - MWC. Pot. Kettle.