Freedom of expression is not freedom to express without challenge. A game is within its rights to include any content it does, but that content is not sacred.
Puppeteer features a boy as the hero, not a girl. Gavin Moore was asked why this is, and his response was fairly snippy. GTA V has three male leads, and fans get snippy when people question this.
Fact is, these two games are totally right to have the characters they have ... but that righteousness comes with strings attached (get it because puppets).
No embed. So, I think GTA and even The Puppeteer are more the types of games where I would much rather at elast try out the female version of a protagonist. Saint's Row, Mass Effect, Dragon Age, and err Tennis games are some of the only games where you get to choose if you would like to play a female version. Even CoD: Ghosts is jumping into the fray, with having the option to choose a female shooter in the multiplayer.
So, at least with The Puppeteer. A game that is supposed to be so juvenile, fun, scary and adventurous, and is supposed to be inviting ot the player. So much that the mildly simple gameplay is certainly even targeted at all ages and genders, and such. So, well you can't choose. Boy trousers for all, and that's that. Weird stuff.