Amy and Rory's life in the present time period isn't really an open storyline. It's pretty clearly closed. They chose the Doctor over that life and then they got zapped back in time.
Brian isn't exactly an open storyline, but it's a shame that he won't see his son anymore (then again, neither would the parents of any companion who died).
River and the fields of Tranzalore are likely still yet to come. The gaps in the Doctor's life was for a specific story reason and because it allows flexibility if they later want to claim something happened in the 11th Doctor's life that we didn't see (and for books, audio dramas, and fan fiction).
ETA: For what it's worth, I liked not seeing Amy's family. The show is about their travels, not their family. I thought having Rose's family was a nice change of pace and I liked Donna's family so it was worthwhile (Martha's family were relatively pointless), but it isn't necessary each time.