I just think it's blown way out of proportion. we know that Ueda like minimalistic fairy tale theme with his games, his character in previous has obvious gender roles/stereotypes in it. Ico is a boy doing all the puching and climbing while he help the fragile Yorda. Wanda is the male warrior doing all the climbing and killing colossi while Mono is sleeping waiting. just like the old fairy tale with prince charming saving the princess.
so imagine you're Ueda thinking to develop Last Guardian, by default he think to make the main character a male because that's what his previous work has been. then he think of the possibility of main character to be a girl, at this state, his mind is still within the gender stereotypes of female being the fragile feminine character, so it'll wear skirt and have less stregth than a boy, then they come with problem of player seeing underneath a skirt etc. at this point, why make the main character a girl at all if she'll dress like a boy, and have the strength of a boy,and serve no other purpose for his story.
I think it's a very logical train of thought. I never felt Ueda is being sexist when he explain the reason why it's not a girl.