"We wanted to be able to tease on Nilin's private life, and that means for instance, at one point, we wanted a scene where she was kissing a guy. We had people tell us, 'You can't make a dude like the player kiss another dude in the game, that's going to feel awkward.""
While I have absolutely no problem with female leads per se, the above mentioned quote raises the relevant issue (for me at least). I do have problem playing as a female character in anything even remotely sexual (eg. a kissing scene) in games. My character in ME is male for this reason. And I don't have any problems with Lara Croft as TR is (or was, haven't played the reboot yet) about exploration, not a personal story. Mirror's Edge is another good example. Add FF13 too.
All this leads to "Female leads don't sell", since many people (according to publishers) have these kinds of reservations.
And likewise, it isn't surprising that most games don't bring in a significant female crowd, probably for the same reason.
I think they are avoiding the issue. Beside a few niggles about female characters (mentioned above), I would totally play a good game with strong female lead.