My problem are the open story lines:
1. Brian Williams
2. The Fields of Trenzalore
3. Amy and Rory's life back in 2012 (or 2020, whatever)
5. The inbetween bits with the Doctor (he aged three hundred some odd years and we weren't a part of it!)
But my biggest problem was that it felt like a half assed good bye, like the PTB were just dumping them off. I felt the emotion, but I kinda felt like it was forced. One thing I do miss is the familial part of the current Who, Rose and her mother, Martha and her parents, Donna and her family, with Amy we saw her family, maybe once for five minutes. That doesn't really work for me. Doctor Who in the Tennant era was a very human experience with family and emotion working alongside the fun, this is turning into your run of the mill sci-fi adventure. It's becoming generic and it's almost becoming forgettable to me.
I actually quite liked that we saw Rose's home life, I thought it was an interesting new take on a companion, unfortunately I didn't need to see it with every single companion, nor did I need it to be so similar (the harridan of a mother and the weak father). I hope we don't see any of clara's family, which doesn't mean I want us to never see a companion's real life again, I just don't think it needs overdoing, and doing all the time.
Of course this isn't a nu Who thing really. Nyssa saw her father often