The Last of Us has been out for a while now, which allows the game's developers to start letting loose with the behind-the-scenes making-of postmortems. The game was originally conceived as a pitch to George Romero back in 2004, combining the escort missions of Ico, the limitations of chronic heart disease suffered by Sin City: That Yellow Bastard lead John Hartigan, and the world of Night of the Living Dead. Romero ended up turning the idea down, but the concept went on to evolve in the imagination of Naughty Dog programmer Neil Druckman for years to come.
The game went through many iterations from there, with the heart condition gameplay elements going by the wayside, and many different prototypes for Joel and Ellie. At one point, the game was called Mankind, and the plan was for the [Spoilers] plague that destroys human civilization and transforms people into savage monsters [/Spoilers] to only affect women, with Ellie being the only woman who's immune.
A game where you spend most of your time killing women because all women are monsters? That would have made the original "Shoot Black People: The Game" build of Resident Evil 5 look practically controversy-proof by comparison. It's no surprise that the concept was scrapped because "It was a misogynistic idea," though with the critical success of GTA V, one has to wonder if they could have just called it "social commentary" and "satire" to preemptively diffuse accusations of promoting problematic or harmful concepts.
The Power of Failure: Making The Last of Us [The Verge]