The Indoctrination theory would have been awesome and would have been better than anything I could dream of (and apparently better than anything Bioware can dream of as well).
I don't think they can really fix the ending if they're going to stick to their ending as-is and just expanding on it. (secretly hoping to be proven wrong)... Actually, to be honest, with how they built the expectations up during the development of ME2 and ME3, I don't really think they can fix the ending in any way to satisfy expectations now. With everything Bioware said, I was actually expecting a game where choices in the first two games had the kind of impact that will cause the story to branch out... almost like Witcher 2 after the first chapter.
One of the big problems for me with how they made this game (and I've probably mentioned this before), is replayability... Where I played ME1 and ME2 probably over 10 times each, I don't see myself playing ME3 more than 3 times... and this game had the potential to keep me busy for a year. I've played the game 1.5 times so far so I'll just finish that half game when they release the DLC and that experience will determine if I'll at all be bothered to play through a third time.