The following was taken from a text I found on the web from the creator of
NGE.

The True Meaning of Evangelion

I've noticed, of late, that there is a growing number of people who believe
Evangelion is, in fact, the Biblical story of Revelations filtered through a
post modern, post apocalyptic, science fiction future. The average fan
understands, with all of his or her heart, that Evangelion is actually a
manifestation of my conscious desire to make an impact on the world, and
that Shinji is my reflection, a forum in which to deal with my own
psychological problems of inadequacy and powerlessness in society. While I
deal with my apparent mental problems, I appear to present numerous themes
and common conflicts, such as man's innate desire to harness nature, a
conflict between creation and creator, a conflict between father and son...
man versus man, man versus himself... Apparently, Evangelion is viewed as a
philosophical and creative masterpiece.

This is wrong.

The true meaning of Evangelion, straight from me, the creator, is as
follows:

Sexual repression and fulfillment.

There is a boy, Shinji. He wants to fuck his mother (Rei), his guardian
(Misato), and his hot redheaded fellow pilot (Uh... Asuka). Throughout the
series, he finds himself unable to do so, a mental block represented by the
fact that he can't even have proper wet dreams. Eventually, lacking sexual
fulfillment, he moves on to briefly experiment with homosexuality (Kouru).
This doesn't work. He's sad, and kills his would-be gay partner in a fit of
intense frustration.

The last episode, where Shinji ends up happy and content, is mistakenly
assumed to coincide with the end of the movie End of Evangelion: not so. In
fact, the entire thirty minutes occur in Shinji's mind around the BEGINNING
of the movie: depressed due to his serious sexual malfunction, Shinji
discovers masturbation, a revelation brought forth by gazing on Asuka's nude
body in a hospital. The moment in episode twenty six where everybody he has
ever known applauds him occurs at the same exact time as that of climax, a
figurative representation of his newfound happiness, fulfillment, and peace
with the world. In the end, it must be understood that Evangelion is NOT
about man's inherent nature, but the fact that one boy cannot get any, and
finally discovers the existence of his hand.

Thank you for your time.

-Hideaki Anno