It's not the quantity of women, that's a red herring, it's the quality of women, and the changing of good female protagonists to, yes, equally good male protagonists, not to help the story but only because they think it'll sell better. And they only think it'll sell better because games with female protagonists haven't sold well in the past, despite the fact that they have much lower marketing budgets on average. That lower budget being because apparently female-protagonist games sell badly. If they still sold poorly, all else being equal (quality of game, marketing budget, that kind of thing) then they would have a reason. As it is, that's just prejudice and/or poor/lazy reasoning.
It wouldn't really MATTER if there were only 30, 20, 10% of games had female protagonists, as long as they were actually people, the same way male protagonists tend to be. Instead, we got the two stereotypes of the Bimbo-Who-Is-Inappropriately-Sexualized or the Tough-Independant-Woman-Who-Don't-Need-No-Man tropes, with like one or two exceptions for every 10 or more stereotypes.
That's another thing. Except in physics, in which case they're from a faulty equation, exceptions exist. It's why we deal in statistics, because it's the TREND that matters. If a hundred studies on evolution are true, then it doesn't matter if there was one fraud a hundred years ago, that one fraud doesn't topple the whole thing. Same here, if there are hundred stereotypes in games, it doesn't matter if there's one Alyx Vance or a Samus Aran here or there, it doesn't topple the trend.
That's all I want to say for myself on the matter. :3
*Numbers pulled out of ass, if you focus on them then you're an idiot.