It needs to be said that the moment a protagonist displays a behaviour that is intended to 'represent' one subset of people, intentionally or not, it is almost certainly offending or annoying someone.
I suppose the way I see it is, imagine a game with an LGBT main character, you are left in one of two positions, you can either just state that and have the character act just like a normal human being, which is the 'realistic' method, or you can leave 'indicators' in the game such as mannerisms and dress. The advantage of number 2 is that it leaves the player no choice but to accept who that character is, the negative side is that, in order to make the situation clear in the simplest manner, the cliche toolbox is often used.
Someone who, after a battle, says in a camp voice 'Ohh, weren't you a tough one!' to indicate their sexuality, might get the message across, but does it do so in a way that is healthy? I know many people who have slightly camp voices but are not members of the LGBT community, A does not, in any sense, mean B, it's just a story-telling tool that is past its sell-by date. In this respect, FF are bang on the mark.
The problem is the fact that patriarchalism and misogyny are being identified as the source of the problem when they are in a way as much a part of the symptoms of it.
We've ended up with a situation where there are a lot of people getting annoyed at the mis-representation or stereotyping of women in games, and quite rightly so, and then pulling out comments about 'Mothers basements' and 'Neck beards' that mean they are reaching into precisely the same toolbox.
Everyone wants a nice easy target, Feminists, Girlfriends, 'Gamers' etc but it doesn't work like that, and every step where we identify 'traits' of those we stand against, we are just as guilty of building a model based on our own perceptions as those who think that women 'belong in the kitchen'.