When I was reading the latest update to HPMOR, I was upset to feel that the Hermione character was veering into disappointing territory. From the beginning of the story, I thought that Hermione was an awesome character, and I've been waiting for her to have a more active role. For one, I think this would make the story more interesting (I dislike that Harry and Quirrell do nearly everything of importance). Additionally, however, society as a whole has an idea of men as active and women as passive that is very problematic and doesn't need to be reinforced.
Of course, EY has not finished his story yet, so I hesitant to pass judgment on an incomplete work. Nevertheless, he has indicated that this story is swiftly drawing to a close, yet we have not seen a single female character burst from her cocoon into the butterfly of rationality.
The male characters in this story have more leeway for flaws because, for one thing, there is an automatic real-world assumption that men are more capable (of nearly everything!) than women. If you disagree with this, merely turn to much of the discussion surrounding Hilary Clinton's presidential bid. Within this story itself, the best examples of rationality are Harry and Quirrell (and now Moody, it seems). Neither Hermione nor McGonagall operates anywhere near the same level as them on the spectrum of rationality. EY drives home this fact by having McGonagall constantly remarking on her confusion.
In a cultural vacuum, this situation wouldn't be a problem - if there are only two "successfully" rational characters, then it doesn't seem unlikely that they both be male. I am not accusing EY of any malice or purpose. In fact, that is just the problem. Male is the default I'm our society - I go to an Ivy League college, and even there (a bastion of liberalism!) the school store has a "clothing" section and a "women's" section. Not a "men" and a "women's" section. This kind of default to the male experience and the male gaze is persistent, insidious, and harmful. If EY and Less Wrong are truly interested in making the world a better place, optimizing, increasing awesomeness, etc., then it seems like this is a relevant area of concern. Just as seeing positive portrayals of gay people in mass media make individuals more accepting of homosexuality, seeing active intelligent portrayals of women decreases sexism.
That's why, for as much as I love HPMOR, reading it makes me sadder and sadder as the story progresses. Some of the comments in response to Alicorn's criticism make me sad, too. I think what my Feminism, Gender, and Sexuality Studies department calls "male privilege" is really just an example of irrational thinking.
I have no idea what EY's plans are or what his intent is, but I know how this story seems right now. It seems like HPMOR is defaulting to male, when it would have taken only a little bit mor effort to include more positive female representations and make the world a little bit better place.
Edit: Please excuse any grammatical errors #Damn You Autocorrect