Check this out: http://www.gamesindustry.biz/articles/2012-12-12-naughty-dog-theres-a-misconception-that-if-you-put-a-girl-on-the-cover-the-game-sells-less
Sony was being sexist and told ND to take Ellie off the front cover in order to be more manly (it never explicitly mentions Sony, but what other "higher up" company would tell ND that?).
Someone else can make a thread about this if they want, I don't want to start a flame war thread. :P