I find Matt Smith to be a very humorous Doctor who can be serious while keeping that playful smile about him. That's what makes Smith unique as The Doctor. I really had my doubts at first, but I've enjoyed watching him go throughout his journey. The Ponds and Rory have also been fantastic companions. Rory really surprised me in how he's grown, and just how unique he is. Amy is also far from my least favorite companion. River is just awesome.
As for the Rory being The Master thing, it's somewhat plausible. Consider River first: could having some residual time energy really create a half Timelord child? Even The Doctor wasn't really able to explain how River came to be. She's an anomaly. If Rory happened to be The Master somehow, then there you go, a half Timelord child.
In Let's Kill Hitler, Amy tries to write off the pounding, but the pounding isn't acknowledged by anybody else. On top of that, Rory specially mentions the pounding being in his head. That's more than a little bit suspicious. It isn't entirely conclusive, but it can't just be ignored either. Subtle hints seem to be the name of the game when it comes to major, multi-season plot points in Doctor Who.
Finally, in The God Complex, how is Rory the only one who has no faith in anyone, or anything? He's supposed to be human, and no human has no faith in anybody or anything. It would make sense for The Master to have no faith. Everyone and everything has abandoned him, and he's learned to rely on nobody but himself. I'd say Rory is a rather odd character. Plus, consider him being The Last Centurion. The Doctor plainly said that 2000 years of being constantly awake would drive a man mad. There was nothing wrong with Rory's consciousness after all that time. He may have been plastic, but he was still all Rory mentally. It would take someone with an extraordinary mind to last that long. Nobody else has an amazing mind quite like a Time Lord does.
Still just conjecture, all in all, but I feel like season 7 is going to be one hell of a season.
By the by, after this Doctor goes, The Doctor will be in his twelfth regeneration. This is supposed to be the last regeneration a Timelord is able to go through. It was mentioned by the writers that with The Doctor being the last, the rules may no longer apply to him, though I thought the regenerations were a genetic thing (such as when River used up all of hers to save The Doctor in Let's Kill Hitler). Hopefully the writers don't do some weird thing that makes no sense to keep The Doctor going forever.