I sort of feel like I wasn't watching the episode closely enough. I mean, considering Eleven had been trying so hard to insure Amy and Rory spent time together in the previous episode - I just felt like I wasn't reading the Doctor's POV right in "Amy's Choice."

It's always possible that Eleven is just not trying to think about it too hard - the Doctor is known to run away from things after all. Eleven is clearly conflicted over Amy and Rory's relationship...he's not sure where he stands there.

But I'm glad I'm not the only one who came to that conclusion...cheers! :)