I noticed something on re-watching The Time of Angels/Flesh and Stone.

WARNING - FLESH AND STONE SPOILERS!!!

In Flesh and Stone, pay attention to the Doctor when he leaves Amy in the woods with the clerics.

His jacket has been taken by the Angels before he entered the forest. He has to leave Amy, and tells her he'll be back. He leaves with River and the Bishop/whatever. Amy says something like "You always say that."

Then the Doctor returns ... but he's acting completely different, worriedly looks back the way he just left ... and he's wearing his jacket. He asks her what he told her when she was 7, she says she doesn't remember and asks what it was. He gets a pained look on his face, kisses her forehead, and says that isn't the point - she has to remember. Then he leaves.

The next scene is of the Doctor, River, and the Bishop walking toward the flight deck as if the Doctor hadn't paused to talk to Amy a second time at all. And he doesn't have his jacket.

I think it's because he didn't. The jacketed Doctor is the Doctor from the finale. Remember River showing the Doctor how to land the TARDIS silently? He used this information to talk to Amy without her realizing that he's just shown up from his/her future.

Also, note that in The Eleventh Hour, at the end, 7-year-old Amy looks up and smiles when the TARDIS sound is heard, as if she hears the Doctor returning. We then see 21-year-old Amy wake up in her bed. I assumed at the time that 7-year-old Amy was a dream at this point ... but what if she wasn't? What if the Doctor actually came back to her when she was 7, but, because of the effect of the Cracks, she doesn't remember?

SPOILERS END.

I think this season is going to turn out to have a much more well-constructed overall story arc than the last four have. Obviously, this remains to be seen, but based on the fact that I'm so carefully picking it apart in the first five episodes of the season (which would have been impossible in the last four seasons), I feel like it's much more well-planned-out.