This isn't easy, guess I'll just summarize what I have gathered about each class, partly for myself and partly to make it easier for you guys to help.
Agent: everyone says good story, but until lvl 15 I have mainly been fighting small fires for the higher ups, and protecting an empire as ridiculous as it is evil isn't the best motivation.
Inquisitor: Again everyone says good/best story, but until lvl 15 I haven't seen much to support it, the quests where standard and usually didn't reveal new info. Also I'm not a big fan of magic super thingies, or magic doing anything a sufficiently pissed of elephant can't do, and it seems like the main plot is going to have me chasing magic things to do something rather grand. Oh,
and my master will back stab me, thanks heavy handed foreshadowing.
That said, it has potential, since it seems like it's the inquisitors that run the show in the empire, so maybe the plot will make me feel a little more in control than most of the others eventually.
Warrior: So far I have liked the missions (Grathan especially), and while the main plot seems a bit meh (stopping a jedi), I have really enjoyed the fact that my class missions have shown something new (like learning who was behind the slave rebellion. I'm a bit concerned that I'll just end up flying around the galaxy as muscle for the siths, without ever feeling like I affect much or decide much, especially if the missions become more standard and bland.
Bounty hunter: Main plot is rather uninteresting, however, like the sith warrior, I have really enjoyed most of the missions so far. While they don't reveal anything new like the warrior, they have been some of the better ones. Again, like the warrior I'm worried that the quests will become more bland, and since the main plot is probably the worst of the bunch, I'm not really sure.
@Mim: I tried to use my smuggler as a tank today (to get the rakghoul disease, which I wasn't able to get, wasn't the disease supposed to be terribly contagious?). It was, eh, interesting. Made me wish that the shotgun could be used a lot more frequently.