The Indoctrination theory made a heck of a lot more sense than any of the other endings. Heck I thought that's what was going on during the whole game anyway with the kid appearing through the whole thing. It seemed like the way brainwashing had been done before. Take something familiar, and twist it until you no longer understand why it would be twisted to see it that way.
The rest of the game however was wonderful. I think that's why the end felt so bad. If that had been the ending to something like Doom, whatever, Not that personally invested in the characters. Not that invested in all the other people. If the story from Mass Effect 1 through Mass Effect 3 had not been so well thought out and engaging, the ending of ME3 would probably have never been an issue.
"I would rather be exposed to the inconveniences attending too much liberty than to those attending too small a degree of it." Thomas Jefferson