Spoilers below cut
First, I am having the problem that the Daleks get repeatedly undestroyed. The entire race of Daleks was supposedly killed three times now, and they keep coming back. Now with a parliament and esthetics and and a morality system.
But this is not problematic if handled well. And the episode itself was fine. My problem is that Moffat, who wrote this episode, has really fallen into a formula that includes:
1. Lets do awful things to Rory and Amy to show their relationship under stress, because apparently showing their normal relationship functioning would be too boring. How could we know this was an epic love unless we see it under some kind of ridiculous stress every week, right? (Sometimes I think there hasn't been a decent, comfortable married couple on TV that are allowed to be a comfortable, married couple for an entire episode since Wash was killed.)
2. Lets infect the characters with something. Because normal tension is not enough.
3. 5 minutes before the end, we must have a "big reveal" that shows that is designed to totally blow your mind and flip all assumptions: the ship is really a volunteer you don't have to torture, the child is really an alien, it's not really Amy, and its not really her baby, the Doctor is wearing a doctor suit.
So it no longer surprises me when the human turns out to be a Dalek. I'm sorry, Mr. Moffatt, but you have just gone to this well too many times. I am now waiting for the big reveal at the end of your episode.
So while it was good, I'm starting to get annoyed at seeing the same trick over and over again.