I'm all for the indoctrination theory, there were just so many hints along the way that I can't really imagine it being anything else. From an email about Indoctrination, to the dreams, the child, the settings.. it's all been said before, much better than I can say. Just look up some videos on YouTube. One thing I have considered, however, that I haven't seen elsewhere is that 1) Shepard was never fired at by Harbinger and 2) Shepard never left the beam.
I think Harbinger takes over as soon as Shepard is close enough, making him believe he's been injured by firing an illusionary blast. If you listen to when it happens, it sounds different, Harbinger makes a rather odd noise, and then there's a high pitched whine like ringing in the ears. The next moment, Shepard is waking up apparently injured, missing his armour and weapons, and there are trees and bushes around him that didn't exist before, but do exist in the dreams he had.
Shepard moves slowly to the beam, shooting a gun with unlimited ammo at a few enemies. If you look carefully as you approach, the area matches up extremely well with the rubble in the 'breath' bonus scene, so obviously he didn't go any further than this point. My thought is that the Crucible/Citadel is controlled mentally from the ground, he never actually gets ported up to the Citadel at all. The Reapers and the ones that made them were all capable of mental control, and considering the Citadel explodes when the Crucible fires, it's pretty sensible not to be standing on it when it goes off.
So you have Harbinger placing illusions into Shepards head, making him believe he's somewhere he's not. If you look at the point on the Citadel where the control panel is situated, the circular floor looks exactly the same as the circular floor at the base of the beam. So parts of reality are leaking in to the illusions, as Shepard fights for control. The rest is well known, with The Illusive Man being Harbinger, while Anderson is the part trying to fight, with Shepard acting as the mind it's all happening in.
Once the battle for the mind is over, the child appears, which is Harbinger trying to influence the decision on what to do with the Crucible. The child states that it can't make the choice, it can't fire the Crucible, so Harbinger needs Shepard to be able to make the choice for it. It tries to influence him away from Destruction and to one of the others, Control or Synthesis, both of which lead to complete indoctrination and a win for the Reapers, as they get to live.
There's a lot more proof out there, you can watch movies on YouTube all day and still find out more. I don't see the ending any other way, it's simple trick of the mind indoctrination.