Doctor Who: 10 Storylines That Will Never Be Revisited
9. Madame Kovarian's Whereabouts
Madame Kovarian was the big overarching villain of Series 6, and along with the Silence, she was responsible for turning River into a murderous psychopath, as well as the Doctor's "death" on the shores of Lake Silencio.
In the finale episode, she was killed by Amy as revenge for messing with River, which seemed to put an end to Kovarian once and for all. But then the events of said finale were wiped from continuity when time was reset, meaning that Kovarian (and, presumably, some of her loyal Silence followers) is still running around out there in the Whoniverse, possibly plotting another evil scheme.
Now sure, villains get abandoned all the time in Doctor Who, but Kovarian had such a raw, unbridled hatred for the Doctor that it's really hard to believe that she'd just leave him alone, especially after discovering that her plan had failed and he was still alive.
Unfortunately, Kovarian was a Steven Moffat creation, and since he's no longer with Doctor Who, it's highly unlikely that we'll ever see her return. Not that other writers can't use villains they didn't create, but Kovarian was so intrinsically tied to River, Amy, the Eleventh Doctor, and Series 6 in general, that it would feel really weird to have someone else try and pick this thread up.