Wow, and here I thought I was the only one who was crazy enough to actually seek out games with female main characters. I love being able to play as my own gender, and as a gamer that's a problem sometimes.
For instance I love RPGs, they were some of my favourite games from childhood (JRPGs mostly), however as I got older I became less and less interested or invested in the characters (the female love interests in particular annoyed the hell out of me).
However after playing KOTOR, which let you choose your gender, I was actually able to connect with my character, and become invested in the story. I've never been able to get back into playing JRPGs(though I've got to admit I'm in love with the Persona series, the P3P gender choice just made it that much better).
I think the problems that I experenced arose from exactly what those JRPG protagonists were, which were basically player avatars, a husk of a character into which the player inserts himself. This didn't change when I played KOTOR, but this time I experienced it as a female, which let me feel how all of those male players must have been feeling while playing as a male protagonist.
As for other genres (I admit I'm mostly an RPG player) I do often wonder why there can't be more protagonists like Jade or April Ryan, genuinely sympathetic well-rounded female main characters. I love half-life, and I've often wondered what it would be like to play a spinoff starring Alyx Vance for example, or maybe the next Zelda game featuring a female incarnation of the hero of time. I realize the whole legacy of the "games as a boys-only medium" is still pervasive in the hardcore market, but a little variety would be nice.