So far I've finished the stories for 4 characters, Warrior, Inquisitor x 2 and Trooper) currently working on Agent, Consular and Smuggler.
Out of the 3 Stories I've played through I have to say Inquisitor is my favorite by far, though I'm a bit biased with that because Khem Val is my favorite companion and I find his quest line very compelling and decently thought out. I've read a few of these "Best Story" threads and find that a lot of people would disagree with my opinion that the inquisitor story is one of the best and often describe it as cliche, etc, etc.
In a way I agree and disagree with them, yes rising to power from being a slave is a bit typical but looking into things further on as the story goes, you see how the character can actually suffer from acquiring too much power.
(Possible Major Spoilers ahead!)
The way they implemented it, although we don't actually get affected by it gameplay wise makes me think that yes, the character may gain power, but at quite a large price.
Warrior's coming in at a close second though, as the plot twists and companions in that story were really great, and I'm thinking about playing it through again.
I don't see why the Consular story gets so much hate, I'm only up to act two but so far I'm enjoying it, don't know if it could be because I'm playing as a light side Sith Pureblood and the species sort of sticks out, but I like it and think that it actually fits quite well.
Just my two cents.