Honestly, I think Bioware did that fucked up ending on purpose just to stir up the whole internet. It's a viral marketing campaign packed in a complete game. And two or three months later they clear everything up, tada, Shepherd was indeed indoctrinated.
If they were indeed planning this all from the very beginning and the endings were just a viral marketing gag, I say mission accomplished.
updated: 14.01.2012
playing right now: Xenoblade Chronicles
Hype-o-meter, from least to most hyped: the Last Story, Twisted Metal, Mass Effect 3, Final Fantasy XIII-2, Final Fantasy Versus XIII, Playstation ViTA
bet with Mordred11 that Rage will look better on Xbox 360.