I think it could make sense for Amy to be a hologram/replicant/otherwise not real. There's been significantly less information about her background than there has been with the previous companions, each of whom had at least two highly visibly family members--hell, we even saw that forehead portal dude's mom. This could be a difference in writing styles, with Moffat being more reserved when it comes to character development, but maybe there simply is no backstory to know about her. Whenever you have a story featuring a character who was not raised by his or her biological parents, it's a given that you find out why, and there is no why with her.
Perhaps the name change from Amelia to Amy is significant. It's possible that young Amelia was real and that adult Amy is a fake. (Maybe the 30/11/1990 on Rory's name badge is when she was born?) Regardless, there's something off about the village that we see in The Eleventh Hour. Everyone knows who the Doctor is, and the duckless duck pond could be a result of the replicant programming not devising a sufficiently detailed world. Either way, her house is jacked-up:
Which leads to the subject of the TARDIS. As this article points out, Van Gogh's painting may well depict two TARDISes colliding. The jacket situation could mean that there are two Doctors, and the second one crashes into the TARDIS that River Song is currently in while the other is locked inside the Pandorica. TARDIS technology has been more visible than usual in this series. In the above screencaps, exterior shots of Amy's house show a two-story building, while interior shots from both ages show stairs leading to a third floor. Maybe there's not a library and a swimming pool, but the house appears to be bigger on the inside, and if it has TARDIS-like qualities (besides a blue door), that would explain why the photo of Rory was preserved, much as the ring was preserved inside the blue box. It's stated that sometimes things are missed when a person is erased, but River also makes a pretty big deal out of it.
Additionally, The Lodger may not have been as much of a lighthearted fluff episode as it appeared to be. The Van Gogh magnet on Craig's fridge could have been foreshadowing to his role as messenger. The crack is visible in Craig's house, even though Amy wasn't inside, and a crack appeared on his arm after he touched the mold that was actually where the fake TARDIS was attached to his roof. He wears long sleeves in the rest of the episode after that, so you can't tell whether or not it went away. Craig also insists that the Doctor keep the house keys, and the Doctor responds, "I might pop back soon, have another little stay?" The Pandorica Opens showed brief returns from other one-off characters, and as the crack showed up at Craig's house, the Doctor may need to visit him.
River Song's presence should also be considered. At the moment, there is little reason to believe that she is directly involved with the events of The Pandorica Opens, as she's as in little control as anyone else. If there are two Doctors, then the switch was made during her previous appearance. Also, there's a viable vortex manipulator out there somewhere, and considering that Moffat wrote Captain Jack's introductory episodes, maybe the reference should be taken seriously.