Isn't this discussion getting a little bit old? Women in games are slowly becoming more and more realistic, just as men in gaming. The difference here is that the stereotypical male traits (strength, independence, pro-activity etc.) have positive associations in our society, while the female traits (caring, empathy, obedience etc.) are seen as positive but not as strong or important as the male traits. The same goes for the body stereotype, the male is a burly, muscle man with a jaw of stone and solid features. He is something the average joe can aspire to look like and feel good about himself because this man is strong because he wants to be. The female stereotype is a slender and with curves "in the right places", her face is cute or sexy and she wears clothes that shows off her body. She does this not necessarily because she wants to, but because it is what is expected.
The problem, I feel, is not that games provide us with "bad" female stereotypes. The problem is that the female stereotypes are taking a lot of flak today. I am not saying that I agree with the female stereotypes (as I myself tend to break away from them), but rather that we still haven't found a good stereotype for the modern woman. The old subservient woman who acts in order to please "her man" is more or less outdated, but there is no real stereotype to replace it. On a societal level, it is a good thing since it allows women greater freedom, but for the average sub-par story writer in a gaming company it makes it very hard for them to make an easily relatable woman.
See, making a good character in a story is not about making them realistic. It is about using stereotypes in a subtle enough manner that people connect to them and recognizes them. Alyx Vance is a perfect example of how you can blend various stereotypes to produce a result that most gamers feel is "realistic".