I think part of why people seem to like Clara is because they think the Doctor is in love with her...
Although honestly what straight male wouldn't want to get Clara into a snog box? Just re-watched Bells of St. John today and I think as her first 'real' appearance I think she had the best 'intro' episode of all the modern nuWho companions. I mean really, she's not introduced as a child or some lonely shop girl or a lonely spinster or even a blatant sex symbol - yet she ticks a lot of the boxes that made companions like Rose, Martha, Donna and Amy not only fun, but almost romantic foils. Its like she's got a little bit of all the modern companions wrapped into one petite package. The wide eyed awe of Martha, the sharp wit and quick tongue of Donna and Amy, the attractiveness of Rose and Amy and yet while she's not the brainy med student Martha was, she seems like a bright girl. Plus the way they shot that episode, the little touches, the music, the way the Doctor doted on her, they were clearly setting up a love interest for him. Sure we all know River and the Doctor at least end up together for a bit - but I think he does still miss having a human to care about. Even though he knows inevitably they all leave him or they die or whatever - kind of a 'better to have loved and lost than never to have loved at all'.
I mean hell the Doctor kisses her forehead when he gets her soul back in her body before he carefully puts her to bed and starts fixing up things around her, the flowers, the jammy dodgers etc.
So really I do hope that it kinda works how 9/10's relationship with Rose went - was set up in one life but really progressed in the next. After all 10 did technically end up with Rose, granted sure it was the meta crisis version of him that was like half Donna Noble, but still... we can still say 10 and Rose ended up together.
So will 12 end up with Clara? I suppose the only real answer to that is how long the Beeb keeps Jenna on the show.