You know, I bet Amy's presence as the Doctor's conscience would have worked better if the Pond's appearance were more scattered. The Doctor is clearly going out and having lots of adventures in between Pond visits, and it is starting to affect his character and his moral compass. Killing Mr. Filch (or whatever his name was) last week...parading Jex to his death this week.... I kind of wish we could be seeing some of these other Doctor adventures to get a better idea of just why this is happening.
I just get the impression that there is a lot we're supposed to infer from these episodes without having a whole lot of information to go on.
I'm getting vibes of the Time Lord Victorious "arc" we saw in the Tennant specials that ultimately led to his downfall.