Her attitude. Her intelligence. Her, I dunno...gumption? This present-day Clara is fine, but the other two version just seemed a little more gung-ho. The current version is just along for the ride, but I don't get a particular sense of excitement from her.
Now, maybe that's the point of this Impossible Girl. The Doctor stole her away to find out what makes her so interesting, but all he has managed to find so far is a normal, boring girl.
Clara is fine. I don't dislike her, but I don't exactly like her either. She's just there...kinda like Martha.
I agree with Professor Zoom.
Clara isn't really being developed as a character. She is a plot device, a mystery for the Doctor to solve. Unfortunately, he doesn't really seem to be doing a whole lot to try and solve it.
Now, keep in mind that this early into Season 5, I didn't really like Amy all that much either, and she and Rory eventually became my two favorite companions. I also found that liked the early Amy episodes a lot more the second time around. The same could easily be true of Clara. For some reason Moffat's run of Doctor Who is off-putting to me until I go back and re-watch it. Then I think it's awesome.
It could also be that I liked the other versions of Clara better because she was interacting with more familiar characters. Oswin's interaction with the Doctor and Rory was fun to watch, and I enjoyed her as part of the Victorian Era ensemble with Vastra, Jenny, and Strax. It's possible that I just don't find her all that interesting as the new main character without all those other people around.