In FPS you almost never have a choice.
Back in the days you had the choice of playing either male or female more often... having FPS games completely dubbed ruined that I think, developers shied from having two sets of voices/different dialogs for male and female characters. Mortal Coil, as buggy and amateurish the game may have been, had two male and two female protagonists (you might have called it tactical shooter - you were able to put someone in command of your team and order the others to do certain tasks). RotT had three male and two female protagonistst to choose from; Quake two had male and female models, and the default character in the first - single-player- Unreal was female (though you could pick other characters if you felt like it - male and female).
While I prefer playing females in 1st person CRPGs and shooters (if given the choice), it's exactly the other way around with my other favorite genre, beat'em ups - I prefer seeing half-naked males punch each other in the face (while hubby always plays girls, but this seems to be a general rule with fighting games).
I haven't played Gothic 3, yet I thought the lack of women in the first game perfectly in order; in Gothic 2, however, I thought it was a pity that there was just one female playing a bigger role, and that only marginally (Cassia). Since G3 is taking place on the mainland and still has no women, it looks as if PB missed a chance.
And I - though I like Star Wars, but was wary of the concept of a SW CRPG - also loved both KotOR games. Had to be said!