Late to the party, but it doesn't bother me when I can't pick my character's gender, depending on how the game is presented/sold to me. And as I understand it, Obsidian never implied that this would be a full "create your character exactly as you want him OR her" type of RPG. This is "Alpha Protocol, where you roleplay as Michael Thorton."
It DOES bother me when I'm able to pick my gender, but I am then forced to be heterosexual in my dialogue responses. I find it even more infuriating when I am given homosexual responses, but only as one gender (as it was in ME, or so I hear).
/two cents