The problem I'm seeing in this thread is the constant use of the term "gender neutral." I'm assuming (possibly wrongly), that this mean the game treats you the same regardless of the gender the player chooses. I COMPLETELY disagree with this notion. Not because I don't think men and women should be treated equally (in fact, my ideal world would be a "gender neutral" world), but this would be completely negating the role gender plays in our modern world. I'll accept the concession that maybe it shouldn't matter in RPGs or games where you create a character because there is only so much you can do with the world's reaction to the characters that accounting for every difference in skin color, gender, or sexual preference would add on hours, days, or even weeks onto development.
HOWEVER, in a game with a linear story and established characters, gender should NEVER be disregarded. The developer's decision to have a male or female protagonist should be reflected in the world around the character. For example, a game like Silent Hill (when it was good) or even Tomb Raider, the characters SHOULD treat the character differently because she is a woman. That's just how the world works. BUT, if they decide to not have the world focus on her gender, there should be a reason. A good example is Enslaved: Odyssey to the West. Monkey doesn't seem to really give a shit that Trip is female. They bond, and there are even hints that they have a romantic interest in each other after a while, but he doesn't focus on her gender. And the reason for this is because the world that they are in (on the run from mechs, constantly struggling for survival) doesn't allow for such petty differences. if gender roles were still a hotly contested issue in this world, the human race wouldn't last very long. Necessity overrides the tradition of the past.
IN SHORT: Unless the game world is written otherwise, games with story SHOULD focus on the differences between genders, because this difference is quite important to our human interactions, and to simply disregard this for equality reasons would be to deny the reality that surrounds us. Should women in games be treated better and EQUAL to men? Yes. Should women be treated the SAME as men? No. And I feel the same way about race or sexual preference. To simply just ignore this element of a character and how it might affect their interactions in the world around them would be an incredibly foolish decision.