Series 5 theory

Most of this will probably be wrong and is just speculation, but I have been thinking about the story arc for series 5. Put the cracks aside for a moment, and think about the "Double-Doctor".

In every episode of series 5 The Doctor has left Amy at some point, and this has also been brought up by Amy in some of the episodes. Why? Why would Steven Moffat and the other writers have The Doctor leave her, only for a while, in every episode. This point was also made more apparent in "Flesh and Stone" when Amy is left to walk like she can see, whilst The Doctor leaves her to go with River Song.
This then brings up the whole Jacket problem. Why would Steven Moffat make such a big deal about him loosing his jacket? He didn't need to lose the jacket, he could of got away easily and kept the jacket, but he didn't.

Also, in many of the episodes of series 5, there has been a second Doctor character, mean a character with the title Dr. before their name:
The Eleventh hour: Dr. Ramsden
Time of Angles/Flesh and Stone: Dr. River Song
Amy's Choice: Rory (He is a Dr. in one of the dreams)
The Hungry Earth/ Cold Blood: Dr. Nasreen Chaudhry 
Vincent and The Doctor: Dr. Black
Many of those could be just coinsidence, but with the "Double-Doctor" thing from "Flesh and Stone", it doesnt seem so.


That is all I have at the moment, not really a theory, but more what I have seen from the episodes so far