So, there is the theory that everyone is talking about in a variety of places, but best explained
here. After rewatching the scene a few times, there is no way anyone could convince me that the differences in costume and in mood/tone when he reappears are anything but intentional -- this is a future Doctor come back to his timeline to rewrite/redirect events (which is something we're very particularly reminded is a possibility in Flesh and Stone..."time can be rewritten") in order to prevent the catastrophe we haven't yet seen.
We know it's important that Amy remember what the Doctor told her when she was seven. Presumably, this is something that Future!Doctor came back to tell her (the daylight scene where young Amelia lifts her head to hear the TARDIS being perhaps not an imagined but real moment), but she has forgotten it, like Daleks, due to the crack. What I'm REALLY, REALLY hoping is that young Amelia's Raggedy Doctor cartoons/stories somehow wind up being important, tying into the fairytale theme of the season. That she worked the Very Important Thing the Doctor Told Her into the imaginary play of her childhood and that's where she'll find what the Doctor needs her to remember.
But whatever, because whether or not that turns out to be the case, I am so excited about this season, I can't even stand to be around myself.