At BioWare's Mass Effect panel at PAX East earlier today, that inevitable question was indeed asked:
"What about the indoctrination theory?"
For the uninitiated, the indoctriation theory is the belief that the climax of Mass Effect 3 is a series of illusions in Commander Shepards mind, induced by the Reapers through indoctrination; a fate suffered by the series most iconic villains.
In response to the question, delivered by a panel attendee, BioWare's Micheal Gamble replied that "it illustrates how committed the fanbase is."
There wasn't much more said, but BioWare's intent is clear: It's their story and you participated in it, but it was on their terms. It will remain that way.
Fans have been, quite frankly, awful to BioWare in the last two months. They've offered more explanations and started more open dialogues than I believe anyone deserves and they've taken their licks for whatever mistakes were made.
They're at PAX and want to discuss the actual game they made and ignore your silly fan theories? I don't blame them.
BioWare has admitted that Mass Effect's 3's endings were light on details that were for many necessary. By that same token, it's time the fans admit that ultimately they had a creative disagreement with BioWare. I think they'll find peace in accepting that fact.