If you let yourself get emotionally invested there is really no beating the agent story. It has some pretty difficult stuff in it. (Also, the most grown-up and interesting romance in the game, with one of the most interesting companions in the game.)
The smuggler and BH stories kind of mirror each other, in that you are doing your own thing, for your own reasons and get sucked into working for your faction's government because of circumstances. They're both kind of lighter stories, I guess?
I didn't care for what i have seen of the JK story, I found it to be really over the top and unbelievable, to the point where I thought it was a little absurd.
SI starts out strong and then loses momentum after chapter 1, which was a shame, because I thought chapter 1 was pretty awesome. Inversely, SW ended up being interesting, and I think pretty well done, if a bit monotonous to begin with. (Things don't really seem to get interesting to me for the warrior until chapter 3.)
I can't really speak for the trooper or consular lines, I haven't sen much of either, but the little I have seen of the consular hasn't impressed me.