Trooper however, now this story is great. Feels like your character has a soul and brain.
I loved the trooper story, but I felt it had sort of the opposite problem to your complaints about the JK story. In the end, especially compared to the way the SW/JK/IA stories play out, everything you do feels like it's just all background noise.
The Inquisitor story bothered me because it doesn't feel like there's nearly as much intrigue as their should be. You're a Sith, a creature supposedly built around the idea of deception and backstabbery... and more specifically you're the craftier and more subtle variation of the Sith... but there's none of that actually happening in the game.
Especially weird when put up against the SW storyline, which is pretty much all about Sith politics when you boil it down ( despite the SW being painted as the more brutish of the two ).
Sith Assassin? More like Sith Archaeologist....