[JimmyA]

Going out on a limb here, but I think the surprise ending is that Mass Effect is actually a prequel to Assassin's Creed - look at how the Starchild is dressed: he is clearly a young Desmond Miles. Which is also why he's so annoying.

Seriously, though, I buy the indoctrination ending. Even if it's not the developer's intent, I'd rather stick with this interpretation.

If it is the developer's interpretation, I think it's one of the best game endings ever - the paragon and renegade colours are reversed, no overt revalation - basically, the player is indoctrinated by the conventions of the gameworld! Genius!