Shamus put my opinion into words almost perfectly. I don't like Sarkeesian and her analyses at all, and I think that pretty every much every problem in the entertainment industry stems from the fact that "male" is the default.
I think some of that is because of marketing. Gaming is probably still perceived to be mostly done by teenage boys and young men, and pandering decisions are made accordingly, even if that isn't true. If it indeed isn't, than I think this is the easier problem to solve.
The harder problem, I think, is that I very much suspect that most game developers and publishers (especially the higher ups) are male[footnote]I studied (a branch of) computer science and not even 10% of my fellow students were women. I hear the same from my coworkers at the small company where I work where all ~15 programmers are male. I believe the figure for computer science studies in the US is a little better (around 15%) and the number of females employed in IT is better still (suggesting that if any discrimination is going on, it is probably "positive"). Nevertheless, the percentage is fairly low, and it was even lower in previous years, so the discrepancy in "experienced" people is probably larger.[/footnote]. If this is true, that also explains a large part of why men are so predominant in the things they produce. I believe that if you ask anyone to tell the story they have been making up in their mind, most would have a protagonist that is basically an idealized version of themselves. And even if that's not the case, developers are often encouraged to write what they themselves think is awesome. The alternative is to try to guess what other people will like, and that is usually not a recipe for success, because chances are you'll get it wrong. No man knows what it's like to be a woman. They can of course guess right, but I think it will be much easier for a woman to make a cool game for women than for a man (and vice versa).
The solution to this would be to get more women into the industry. They need to be in positions where they get to make the big decisions, or at least be extensively consulted on how to make a game appealing to their demographic. Unfortunately, that's easier said than done, because as it stands it just doesn't appear to me that many women are interested in such a career. Hopefully I will be proven wrong though.
Gethsemani said:
As for Chell, I feel she's one of those non-examples. She never speaks or acts in any way that is not prompted by the player. Just like Gordon Freeman she's a name and a body without any other characteristics to actually make her a, you know, character. She's not sexualized certainly, but neither is she give any other form of portrayal. In that respect she's not a good example of a female protagonist, simply because the only clue we get that she's a woman is that we can see her character skin through portals, she's got no personality and as such we've got nothing to connect to as audience. Replacing Chell with a big purple cube (a'la missing source engine assets) would not in any way impact on the narrative or portrayal of Chell.
I see this as a big problem. On the one hand, you have people complaining when the protagonist just happens to be a woman and the game doesn't make a big deal out of it. On the other hand, (other) people would complain if it did. According to user @Labyrinth above, a game shouldn't comment on the relative skill/power of men/women in the game world. According to Sarkeesian you cannot make your women pregnant. According to the Tomb Raider backlash, you cannot have them get raped. Even though these are things that women will (unfortunately) have to deal with more probably. Maybe these are extreme examples, but how would you bring attention to the specific femininity/masculinity of a character without using some kind of stereotype? If you don't, then the gender truly doesn't matter and we are pretty much back to the Chell case, aren't we?
FWIW I think Chell is a very good example of a very good female character. She is actually characterized quite well (we learn a lot about her in the games and comic) and I like the fact that her gender isn't
really important. It's just normal. The odds were (presumably also in the Portal world) 50%. She's female, it's normal, nobody cares. In my opinion that is how gender should be treated in most situations. I don't really see how they could have done it better.
To be fair, I agree it's probably not a female power fantasy in the same way that some games are for men.