Shepard was being indoctrinated.
Someone felt this was at the core of the series, Shepard's personal struggle, and so that's what the final victory/loss pertains to. Clearly, the vast majority don't feel this way, and instead the better choice would have been to have this incredibly personal sequence and then a confirmation of the Reaper's defeat/victory, as well as a last look at the fates of your living crew members. What's left is a clever sequence which makes for an inappropriate ending.
And yes, he was being indoctrinated. You don't need a 20 minute video to tell you that the big black tentacle lines, screen distortion, Reaper noises and Shep clutching his head whilst talking to Anderson and the IM were blatant signs of him being indoctrinated.
So yes, I was irked by the ending because it's not where I would have ended it, but I do not in a million years think it should be changed. The epilogue they're releasing should be more than enough, and even then I'm only fine with it because it seems to only be providing an explanation. (Although I do suspect they would have charged for it had there not been such outrage.)