It really boils down to what you, as a person, enjoy.
I started an IA because I read on the forums the story was interesting. I'm picking light and dark side choices based on how I feel about the particular situation, so right now I am more light than dark. I am not really getting in to the IA story as much as I did with my smugglers story, but I am also only on Balmorra and it's been okay so far.
Out of the SW and JK story lines, I think the SW is more interesting but I didn't really dig playing either class that much.
Between BH and Trooper, I like the trooper better. I just enjoy playing that class more as well as the story.
SI and JC, I really like the SI a lot more than the JC, the JC just seemed more boring to me. Also, Khem Val is really cool.
So my ranks, based on my personal preferences in terms of class and story are as follows:
Smuggler
Trooper
IA
SI
BH
SW/JK (feel about the same with these)
JC
Also, I really just enjoy playing republic side more than imperial side. NPCs are just so mean on the imperial side , sometimes I just want to hug a Sith and tell them that it will be okay.