The biggest issue with the story arc is that there's absolutely no emotional fallout whatsoever. Amy and Rory go through this massive, life altering series of events, and it's pretty much completely swept under the rug. Having your baby kidnapped isn't something that you just recover from right away, especially not if she winds up being brainwashed and turned into an assassin, yet there's been almost no reaction from them.
The very next episode after Let's Kill Hitler deals with the relationship between a parent and their child. Amy and Rory's situation isn't even acknowledge in it. Yes, the episode was moved around in the order, but someone should have realized what a huge disconnect there was there (and the episode it was swapped with was The Curse of the Black Spot, which also dealt with that some subject matter). Old Amy in The Girl Who Waited doesn't acknowledge her daughter at all. The scene about the Doctor trying to deconstruct the idea Amy has about him in the latest episode might have worked better if there was, I don't know, even the slightest mention about how traveling with him resulted in her daughter getting kidnapped and he completely failed at trying to rescue her.
It's like Moffat copied all of the worst elements of the Connor plot line from Angel (child who instantly shows up as a full grown character who is pretty annoying), but none of the good elements (the emotional fallout amongst the characters). It completely destroys the credibility of both the characters and the arc itself.