Gendo is no longer afraid of is child Gendo finally finds a replacement for Yui's sweet ass Gendo is no longer interested in causing the apocalypse to bring his dead waifu back, and probably turns his brainpower towards properly averting apocalypse instead so he can keep pounding that ass The world is saved from tang.
Also, Shinji is more confident and comfortable with him/herself and has now a loving father. And this is not much more fucked up than End of Evangelion.