Finished the game about 3:30 a.m., so I really wasn't following much of the starchild's dialogue or logic. I think I was still more pissed about the god awful combat encounters defending the missiles, but that's another point altogether.
That being said. I chose the blue option and everyone knows where that went. I went back and watched the other two endings on YouTube and not much difference, but whatever. Without thinking too much about the logic of the starchild, I liked the ending. Sheppard has to die, I think, no matter what. They did that. Even though it was cheapened a bit by Mass Effect 2's storyline. And I don't mind not having all of the answers. In fact, I wish the reaper origins were never explained. I'd rather they just be a force of nature that shows up every 50K years.
The indoctrination theory does make sense. But reading through the Google Doc posted, some of the things are extremely nitpicky. In fact, everything about Sheppard and Anderson being knocked out the Alliance forces thinking everyone is dead is nitpicky. That's no more evidence of indoctrination than the Alliance being in such disarray they can't find their people on the ground. But some of it does hold true.
Overall, I think I like what they TRIED to do with the ending. It was downtrodden, depressing and had consequences for the whole galaxy. But I think they handled it extremely poorly. It almost reminds me a bit of The Matrix trilogy's ending. It's trying to be intelligent and provocative, but fails at doing so.