I think a lot of people who are upset at the ending need to take a breath and a step back and look at it more objectively. The indoctrination theory may or may not be the intended meaning, but you can't deny some basic facts about the ending sequence:
1) You are locked in slow motion with no GUI/HUD available. This is exactly as it is in the dream sequences that haunt Shepard throughout the game. What point are the dream sequences if not to create a precedent for the ultimately confusing ending?
2) Shepard shoots Anderson in the arm -- the same arm that Shepard is bleeding from after Anderson passes. Shepard's arm was not covered in blood before this. The game goes to [not so subtle] lengths to bring attention to this detail by panning the camera IMMEDIATELY after Anderson passes.
3) In the 'good' ending following the destruction of the reapers, Shepard is shown waking up in a pile of rubble on earth. It is completely ridiculous to assume he survived the Citadel blowing up, burning through Earth's atomsphere and then crashing down thousands of miles when he's already bleeding to death and barely able to keep himself upright.
When an incredibly well written story ends on a very confusing sequence of events that don't add up in any kind of logical manner, it's painstakingly obvious that there is a hidden meaning. There are plenty of clues along the way, and likely there are multiple interpretations to be had. I think it's insulting to the writers and developers to dismiss the ending as just a random series of confusing dialogues with no artistic direction intended.