IDK which story line is the best. i have done all of the story lines for each class, and tell u the truth i like them all and each one is great. I guess for me it depends on the mood i am in i guess lol just my opinion.
Imperial Agent - the James bond kinda mood with theories and Spy hunting
Sith Inquisitor - sinister mood with a twist lol
Bounty Hunter - Honor (mandolerian) and money
Sith Warrior - just kill everything (bad day at work)
Trooper - Duty and service (but Down with the Man (if dark side) lol
Smuggler - Comedy
Jedi Consular - more of a caring and logical kinda mood (but than again don't have a dark side)
Jedi Knight - Duty, Honor, and Service with a lightsaber. (or a real big jerk lol dark side)