I'm not sure about the Indoctrination Theory. On the one hand, it makes far more sense than anything else, because of the numerous plot holes and various other mistakes that arise without it.
On the other, that would, in my opinion, have to mean that they never intended this to be the ending, and right now they're all just acting when they talk about how surprised the reaction is making them, letting the outrage build to a fever-pitch before going, "Gotcha!" and releasing a DLC real ending they always intended. Which, quite frankly, would make me want to punch them in the face, even if it's free.
Because if the Indoctrination Theory stuff is what they intended, and they didn't plan on releasing anymore ending-related stuff, just more DLC to expand the pre-ending stuff, then...that's actually worse than if the ending just is what it is, in my opinion. Far, far worse. Not because of the dark ending impacts, but because it means the ending answers even less. For all you know it was just a dream and you never left! [Insert spooky "Ooooo" sounds here.]
So, essentially. Either the ending is pretty much flat-out horrible on numerous levels, plot wise, logic wise, closure wise, and hey-that's-impossible wise. Or they sold you a game that didn't even have the ending just so they could screw with your head. Or they sold you an ending that mostly makes sense, but answers absolutely nothing at all, not even a sliver.
Not exactly a good option among them.
As to my feelings on the ending itself... They're too long-winded for me to want to post. I did an...apparently 4,054 word rant in anger to rid myself of it since a friend I usually rant to (and who had apparently spoilered himself to ME3's ending after the controversy began to see what it was about, since he doesn't play the series) wasn't around for me to purge my anger directly to another person. Suffice to say that I Was Not Amused.
The controversy on if they should or shouldn't change it and artistic integrity and all that, though, has me quite amused, considering there's at least the one big post-release game example, in addition to the fact that numerous people change an artist's vision before it ever sees the light of day, in gaming, television, movies, and books, to varying degrees. But now apparently video games suddenly loses its controversial Art Card just because ME3 might get its ending changed.
I'm not saying they should. (I want them to. At least, I think I do. I definitely can't sit through that again unless they at least fix the random impossibilities of people showing up where they shouldn't and such.) They should examine how they feel about the ending and the criticisms directed at it (Especially the biggest criticism I've seen made, I think, the one about how they went back on very specific promises and even seemed proud of it and confused at everyone's outrage) and weigh these things carefully with how much they value their ties with fans and fan support. Heck, they don't even have to use that to come to a decision. It's not like artists haven't, as the accusation goes, "sold out" before.
But between this and Dragon Age 2, two of their last three games have generated huge fan backlash, and if they don't consider things carefully, they might find the good will and trust often given to them by fans suddenly dried up.