So I just replayed the ending and got the "perfect" ending. I have to say, that 5 second clip of the rubble with Shepard gasping for breath totally changes the way I perceive the ending completely. It gives a little "what-if" scenario that I am actually quite positive BioWare will be expanding on in DLC. Or even if they don't, it's just representative of the tenacious spark that made me fall in love with Commander Shepard from the get go, and how she just won't quit.
Anyway, the more I think about the Indoctrination Theory, the more I think it's more wishful thinking than anything else. Quite a few of the main tenets of this theory don't really hold up to scrutiny. First the fact that there was a Reaper roar when Anderson calls you away from the vent doesn't indicate that the indoctrination "failed." There are like 17 Reapers tearing Vancouver to bits, is it surprising that one of them decided to roar? Not really.
Then we have the kid and how no one bothered to help him onto the shuttle. I thought that was weird when it was brought up, but I just rewatched that scene and the whole point of it is to show how terrified this kid is. You spend a good 30 seconds getting close ups of his face as he sees his city getting obliterated. Then he runs in fear to board the shuttle. Sure, no one is helping him, but the point of this scene is to show how terrified this child is, before running to "safety." Of course his shuttle gets blown to smithereens, and this affects Shepard deeply (which results in the recurring dream of her chasing the boy). I think the Catalyst showing up in the form of the kid is nothing more than the Catalyst materializing in a form that is important to Shepard.
Then we have the whole "everything in the Citadel is a dream" argument, which can mainly be explained away logistically. Why are there infinite bullets? Well it would be pretty annoying to run out of ammo in that section, especially since one of the final choices involves you shooting at the canister. Why can't you kill the Keeper? Well have you ever been able to kill a Keeper? BioWare would have had to animate the Keeper dying, all for a 2 second gameplay clip. Not worth the programming time or effort. Why can't you kill Anderson? Same reason. Why is Shepard clutching her left side after she shoots Anderson? Fine that's a little misleading, but I assume she got hurt at some point during the entire fight for Earth (not least when she got fried by Harbinger's laser), so yes it makes sense that she is in pain.
Anyway, you get the picture. Would I have liked the ending to be different? Sure, why not. Do I hate it? Not totally. Like I said, that clip of Shepard gasping for air makes all the difference for me - without it I would be a little frustrated. We may not know what happens to her after she takes that breath, but I can at least convince myself that this ending wasn't it. There is more. We may never be privy to it, but there is more. And that satisfies me.