I've enjoyed trooper so far, it's my first playthrough (newbie here!)
I think it just needs the right kind of mindset, I figured trooper story would be just that, soldier in the middle of a war. You do the yes sir, no sir routine as all soldiers do and well, you kind of have to. Being part of the Republic chain of command it's not like you're operating 'outside' of command like Shepard in Mass Effect for example. Maybe the story would have taken a different turn if they did exempt you from Republic command?
I agree though, the story is a bit flat at parts, there's a lack of urgency? Or impact, I'm not sure what. I've only gotten to the bit with Needles, took him down and it was a bit 'meh'. I also don't think much attention got paid to my decision to destroy a strategic resource. Heck I've disobeyed orders (light side) twice and I only got a mere rebuke. Yet, Garza still loves me... She should probably be grating at me saying I need to stop being an idealistic idiot, heh.
Can't wait to try the other storylines once I finish this one.