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).