I've had this mulling around in my head for a while and I really just wanted to write it all down (and hear what others thought about it.) It was all inspired by this image of Eleven saying: "I always come back" and then there was a panel with Sarah Jane Smith and she says "I beg to differ." (/angry face)
"I always come back..."
Point one: This. These words were repeated throughout the series. I think, to show the Doctor's relationship to Amy Pond. He does not want to leave her behind. The girl who waited? She's waited long enough. Look at "The Time of Angels" and how Amy was asking him to go, and Eleven promptly said, he wasn't leaving her. Ever. (There may even be some guilt there, but I'm not sure.)
The Doctor will always come back for Amy. He is concerned with her well-being, he wants her happy (which I'm gonna talk about in the third quote) Eleven realizes the impact that his absence put on young Amelia Pond. He figures it all out and that's what leads him to his choice in The Big Bang...
"You won't need your imaginary friend anymore..."
The Doctor does this, flies the Pandorica into the TARDIS, woo big bang (and he does it FOR Amy). He knows that in doing this, he'll be gone, but Amy's life will be fixed. The wound that he made will be healed. She'll have her parents, she'll have Rory, and she won't need him anymore.
A rather small point here, I know. But, I'm sure someone else can think of something even more clever.
"The Dream Lord was me."
The Dream Lord created those two dreams based off The Doctor. His two fears.
One; the TARDIS no longer working (the TARDIS is his home, his only life, without it--he'd be stuck) and The Doctor not being able to stop / save his companions and himself.
Two; Amy growing up. Annd once again, not being able to save the day.
I know the second one may sound silly, but think about it. The Doctor holds such affection for Amy, I really don't think he wants their travels to end. It reminds me a bit of Peter Pan and Wendy.
However, the Doctor doesn't pressure Amy into deciding which reality is the right one. Once the Doctor figures it out, that they are both dream worlds, I think that's when he realizes that Amy can't stay with him. She has to grow up, get married, have a house and a family. He knows that's the best choice & knows that it'll make her happy.
I know that there are a lot more -- but those were just the ones in my head. Feel free to even argue with some of my points. 8D