Anyway. The Doctor packs Amy into the Pandorica, popping a quick psychic message into her head about what to do when they dig her up and put her in the museum. Problem one: She is dead. Well, it turns out she's only mostly dead, and they're going to blave her into the future because the Pandorica doesn't let you die, among the many other things it's got going on. It'll scan Amelia when she touches it, and thusly restore her adult self using her baby DNA. I think. In America we don't believe in that, not even for Superman.
Problem two: The universe is over. Also, I guess, not a problem, because Amy Pond is the Moffat Lady Device of all time (literally) and because she grew up near to a Crack, she had it seems "the universe pouring through her dreams every night." (Cracks: Not just for multidimensional bleeds, prison containment services, time-sucking tendrils, TARDIS-bits repository, or appearing randomly once an episode anymore. Those damn Cracks are more timey-wimey than even the Weeping Angels when they need to be.) Apparently this made Amy so special that when the Nestene made the copies of the people, she gave them not only faces but also like hearts, and souls. The whole thing.
(Have you read Ender's Game? Quite good, although poisonous to a certain kind of Ayn Rand-leaning proto-asshole. The second book is pretty good too, but then the third book -- and you might be surprised to hear it -- wasn't sci-fi enough for me. In the first one you had like instant communication, that was about as speculative as it got besides the aliens. The second one, you get a person who lives entirely in the matrix, singularity-style, which I didn't mind because she was a cool person.
But by the third book you got people randomly jumping into hyperspace and trading souls around and it turns out that strong theory and quantum theory are all mixed up sort of queasily with this Chopra-ish animist theory where everything is a soul and then further toward a descriptivist magicalness whereby if you go to hyperspace while thinking about, say, a new bicycle, then when you come back bam: New bicycle.
Irritating, and not just because it's cloying and resulted in a lot of creepy asexual sex stuff, but also because it's like, do you really think before Lessa got tired none of the dragons had ever learned to time-travel? Not one of the Dragonriders of Pern in thousands of years ever just really needed a nap? Do you know what I mean at all? Anyway, that's what is going on here. Amy has unconscious powers of memory so very strong that she can just hand out aiuas left and right. To the point of recreating the entire universe. Maybe that's the deal: She just didn't have room in there for a personality of any kind, besides what Karen G gives her. If that is the issue, and the reason she's such a blank slate of a person -- and not, in fact, because "generic girl" is the default setting for boys who write fairytales about girls -- I still don't much care for it.)