I'm not quite with you, Dimesdan. How does these stories taking place after Series 5 help the issue? Besides, they can't be after Series 5, because Rory isn't with them.
Were you not moaning that Amy should know what a Cyberman is in The Pandorica Opens but you think this is during the series run. Easy, this happened after those events. As for Rory, chalk it up to being at home or just exploring the TARDIS. Do you need to be spoon feed these things all the time?
I just think it's a little bit unlikely. Amy and Rory have only just gotten married, you'd think they'd want to spend as much time together as they could.