Claire/Topher and what you wish their story line had been.
I just wished we had something in regards to their storyline, since it was unresolved rather abruptly just as it had begun.
There was something rather deeply fascinating with their dynamic especially after she found out that she was a Doll and that he programmed her the way she was, particularly in the second season premiere when she was tormenting him. I didn't ship them romantically, but I felt there needed to be further exploration of their relationship on the show. I felt it was important to have there be this tension between them, with Claire confronting him about what he did, and Topher coming to terms with his morality, especially since the second season was all about him questioning what he does, it would have added more to his character development as he further struggled with his conscience with Claire being a constant reminder about what he does. I also wanted to see more Claire in general, I wanted to see how she would be handling trying to find herself despite that she truly wasn't her real self, the original the body belonged to, but rather an imprint programmed to always serve the Dollhouse. It would have been a fascinating aspect of seeing Dolls who become self-aware of who and what they were; we had Echo dealing with that midway through the season, but I felt like perhaps we needed more storylines featuring that.
Basically, I wished there had been more with exploring that very complicated relationship which was introduced. I felt like it was a vital part of understanding their characters, of them understanding each other, and it would have led to interesting places concerning the Dollhouse, the concept of self-aware dolls, and how they cope with that knowledge. Furthermore, the conscience of those responsible of doing that to them. It would have been interesting seeing how Topher and Claire's dynamic would have developed had there been a continuous storyline with them throughout the season, and although I know Amy Acker had other commitments, it's still a shame they had to cut it out entirely.