>I don't understand this!

And pseuds never will understand there's no meaning except for whatever you project. Ano was just depressed and used Shinji as a stand-in for himself while Misato, Rei, and Asuka were just the types of women he liked at the time. It started off as a mecha anime about saving the world and then started getting deeper into religious tropes as Ano got more depressed. 20 years later the show still doesn't make any sense, it's the Lain of mech animes.