This was all summed up on the first page, but..
- Bioware have outright denied the indoctrination theory, go digging on the official forums for their posts.
- The "extended cut" pretty much debunked the whole theory even before the developers stepped in. If none of it really happened, why do we see so much of what happened in the future because of those events?
People are simply trying to read too much into what was a rushed and ill-thought out end to the series after the original writer left the project. There's no deeper meaning, it really was as empty and shallow as it appeared.
Oh, this again? Another person essentially telling me to Google some half-remembered thing that they apparently couldn't actually find themselves. Really, if someone could provide me an unambiguous comment from a Bioware employee from a reliable source that the ending is absolutely what happened, that would settle things. (Comments like that it shows how dedicated fans are or that Shepard survived the Citadel explosion are not unambiguous. A post that does not dance around the question and that straight-up says the ending is real is.)