'The Girl Who Waited' is an episode similar to 'Amy's Choice' in many ways, but ultimately 'The Girl Who Waited' goes one step further. It doesn't just reflect the Doctor in the villain, it is the Doctor that's the villain. The only other things we meet are the handbots, and actually, they're a lot like the Doctor too: they claim that they're only being kind, doing what they're doing for the best; which is pretty much how the Doctor treats Rory when he makes him kill Older Amy. What really makes this a dark moment for the Doctor though, is that he knows how it's going to end, and he knows from the beginning. He gives false hope to Rory and Amy, supposedly his best friends, and then ultimately lets one of them die without much remorse shown at all. It's not because he's the villain of this episode, it's because he's betraying his friends, and as Rory says, making them become him. That's what makes this episode such a dark one for the Doctor: he's there to save them, keep them safe, and yet he can do this. And when Rory declares "That's not fair", we as an audience find ourselves saying the same thing.