Well, actually, from a non-linear, non-subjective viewpoint it's been in the right order, but what I mean to say is that I believe the Doctor experienced S7 in a different order than Amy and Rory, as well as the viewer. I made some specific predictions about the order, but I'm not really confident about most of them. Though I will bet my bottom dollar that The Power of Three came before A Town Called Mercy.
This is from The Power of Three (S7E4)
This is from A Town Called Mercy (S7E3)
This hasn't been explicitly referred to in canon, only in hints like the above (which to be honest were pRETTY STRONG HINTS i mean HE SAID IT OUT LOUD WITH WORDS that is NOT A COINCIDENCE), and that means I don't get to officially gloat about it.
But, do you remember how The Name of the Doctor ended? Do you?
That's right. The Doctor (SPOILER ALERT, DON'T SAY I DIDN'T WARN YOU) jumps into his own time-stream.
Which means (and I'm going to call it here and now) that the 50th anniversary episode will take place within the Doctor's own timestream, and it will finally be revealed that he hasn't always visited his companions in a linear order.
Moffat, you terrible, gorgeous genius. Don't let me down.