It's just a case of "all paths lead to Rome". I wasn't so disappointed because I hadn't gotten into all the hype, but after reading it, I can see why people are annoyed. I'm still not, but I can see why others are. Apparently this isn't how it was supposed to be, because there was supposed to be, as they said, "divergent endings".
And I do know what the indoctrination theory is. Although, I think there's some proof of the indoctrination having started well before the last few minutes. The dream sequences? The times when Shepard all of a sudden hears voices (not Reaper voices, but voices s/he shouldn't be hearing, nor can respond to)? The dreams with the boy are so much like the dreams people being indoctrinated described in ME2. And they never elaborate on what kind of voices they hear at any point. The voices of other people, or Reaper voices? Maybe Shepard started the slow fall towards indoctrination after destroying the Alpha Relay, when s/he was at the mercy of that Reaper artifact for a few days!
Too bad that's probably giving Bioware too much credit. It's always fun to speculate, but when you start to speculate, it all boils down to this... Can you expect the people who made the story to be that creative, or are you just grasping at straws there?
Aaand, I meant that there can't be any more sequels after this if this holds.