I believe its mostly an issue of economics. If a publisher thinks that a male lead character is going to sell more games, then that is what they're going to code. Including a female character (such as in MassEffect) requires not only new modeling and voice acting for the entire game, but also a rewrite and re-code of much of the story. That means a big investment.
I agree with casualcolors about the psychological issues, but ONLY in multi-player games that are geared towards imitating reality (such as BF3). You shoot a woman in FarCry2, and I'll admit, I REALLY didn't want to.
Killing female characters is actually pretty common in RPG's, but in this "fantasy" setting, people don't seem to react the same way as if, say, a female soldier in an online FPS were to get gunned down. I'm not saying the reaction is right or wrong, only that it most certainly exists. FPS makers are already under a bit of fire and I don't think any of them wants to be the first to add more fan to the flame by inserting female soldiers.
I think in a single-player context, however, that having a female is really great - - and I'm actually surprised not to see more of it.
Metroid - one of the longest running, most popular games in history has a female lead. Mirror's Edge is one of my all-time favorite games, and the female lead for that story is spot-on perfect.
I would really like to see some more female leads in a serious FPS series.