I figured out Eva a long time ago, and here today I will reveal the mystical secret of the show!
The religious part is pointless, ignore it. And ignore the giant robots as well.
Shinji could very well be a mob hitman, if you watch the show you get what I mean. He just wants to be alone but they pull him back to his job as a hitman/eva pilot. The eva's are just a job as a hitman, and NERV is the family. Rei II is a dream girl he'll never have, Kaworu is the girl (Yeah yeah he's a guy in the show it would make some more sense if he was a woman but meh, bisexuality isnt all that out of the question...) thats perfect, but got killed cause he was in the mob. Asuka is the annoying wife he can't stand, but can't leave. Misato is a friend who is in the family(NERV). Third impact is a culmination of his depression, his self judgement. Oh and Kaji is the FBI informant.
And as for Pen2 he's comic relief.