I know right, my GM went to far. and characters should be flawed, I hate playing shadowrun when people play Mr./Mrs.do-good,
characters need a reason not to be a corporate wage-slave or gang banger. 
I truly believe shadowrun is more fun if players are inclined to be bad. Thanks for understanding guys
-Ex Street Samurai
p.s. to the guy that suggested bioware, i asked and he said no bioware either
I would agree that a game like shadowrun tends to produce flawed characters. Characters with flaws are more interesting in any setting. I am a big believer, however, in whatever game I am playing in, is that the ability to work as a group is crucial. Characters who disrupt group dynamics, and the players who run them, derail stories, crash campaigns, and sometimes even break up gaming groups.
So yes, flaws. Yes, you probably aren't a boyscout, considering you do black ops for a living. But characters who can't work as part of a team are dangerous, and not in a good way. It can get characters killed, can frurstrate players and GM alike by taking the story off the rails, and if pushed far enough it can cause people to drop out of the game.
I don't really know what your GM was up to with this character, and whatever he was going for there was probably a better way to get it. I am not defending the guy. But honestly, a character who thinks he doesn't need the other team members probably would be dead already. Its not a personality thing, it a professionalism thing. He would have gotten in over his head or somene whould have shot him in the back of said head for acting that way. If you make a characters that he others characters will not like, maybr resent, maybe be outright hostile to, its hard to imagine why they would work with him.