Yes, the problem I have with the trooper storyline is how disconnected all the missions are. If I compare it to my Sith Warrior, for example, the primary villain was always right in my face. I knew where I wanted to be at the end of the game and everything I was doing indirectly contributed to getting me there. I also got to really represent a philosophy-- The Darkside trooper might have the pleasure of following Garza's orders, while the light side trooper gets to support the ideals of the republic, but neither of them have the impact of, say, the Imperial Agent's endgame. LS trooper doesn't get to convince Garza to stop throwing troops away. DS Trooper doesn't change anything at all.
Without a strong rival or unusual goal, the trooper really does feel like any other grunt. Sure, you're the one who actually gets things done, but when they write the canon of the history of SWTOR, you could have been a million people while there's only one Bar'senthor, one Jedi Knight who was in a certain vision, one Wrath...
But the gameplay is really fun, so what the hell. On to 50.