Not all of my characters are 50 yet (see sig), but these are my impressions thus far:
1. Sith Warrior
2. Imperial Agent
3. Jedi Knight
4. Sith Inquisitor
In reality, the IA is probably the best written, but I havent played the third chapter yet and I'm a bit of a Sith fanboy.
Really though, the top 3 are A++++ in my book. Maybe I'll say the same about SI one day too. Only half way through Act 2 at the moment.
Finish your IA. The last chapter is epic. It's like James Bond Skyfall.
Of my 50s, JK/IA/SW/BH, if I had to reroll and choose based off the story, I would choose IA. Once I get take each class to 50 I will go back and replay certain classes to see what happens for the other side, light/dark. I will definately replay IA and SW. JK is too predetermined, and I can suspect that light BH isn't too different from dark.