I'm a vet, and I have to tell you, the choices and conversations you get during the Trooper storyline are pretty horrific from a military point of view.
Me "I have been sent by the Republic High Command. Your elite fighter squadron is needed to stem the Imperial advance"
Them "I don't want to. I'd rather sit behind these sandbags and shoot at escaped criminals"
Me "No, seriously, these are orders. You are ORDERED to return to the Republic and help them meet the Imperial onslaught"
Them "nah, I don't think so. If you want us to follow those orders you have to go around and do all this stupid crap on this planet"
Me (IRL) "FFS, can I just club this fool senseless and stow him in my cargo bay until I get him back to civilization"?
Me (In-game) "OK, since the fate of the Republic depends on you following these orders, I guess I'll do all this crap just to make you do that"
It's ridiculous...and the Light/Dark side choices seem to imply that showing any sort of discipline at all is Dark (sure, deserters, have these credits so you can take a shuttle home while your friends, who have ALSO been here 5 years, fight and die without you....+50 Light Side!)"
Basically, from the evidence of the writing for these story arcs, I have to assume nobody in the design/writing team at Bioware understands how military people think, much less why they HAVE to think that way. For most of the game that is of small consequence, but if you have one of your 8 available classes be "Professional Soldier", I think it would be nice if somebody on your team actually comprehends what that means.
Just saying...