The chief editor of GameReactor just answered!
(Tried my best to translate quickly)
=>
"Yes I removed Ellie.
Neil Druckman, creative director at Naughty Dog behind TLOU didnt really like our latest cover despite it being of the studios recent masterpiece. The reason is because I removed Ellie. After a Twitter message from ND, a debate regarding sexism has been sparked, something I'd like to shut down right now. The reason I removed Ellie was purely due to aesthetic reasons. Anything else is just phony.
We removed Ellie because she looked like a .."after"creation from the illustrators side. She was the only thing in the picture that was on a seperate layer and she looked pasted in and a bit like she was cut out and pasted with a less highly detailed face than Joels. We felt that the cover was better this way. Better looking and we found a perfect spot for our headline as well. If ND really didnt want to see their cover without Ellie then the one who sent it shouldnt have sent an image where the possibility to remove her was there as a seperate layer.
In the end its rather funny but also pretty stupid. We once printed an Uncharted cover without Sully and nothing happend there. Same with Jak & Daxter without Daxter. One with Ratchet & Clank without Ratchet and one for Half Life 2 without Alyx. We have also done the same for a Super Mario Bros cover with only one of the brothers and another from Army of Two with only Rios. Its about design, and thats all there is to it."
http://www.gamereactor.se/blog/petter/569231
He's got a point in my opinion. He simply preferred it that way.
