Soviet Heavy said:
I like talking about this, as I have a unique opinion on Eva, which raised my appreciation of it considerably.
It's satire of big mecha anime.
It takes the premise of teenage boy piloting giant war machine in spandex, and just changes one variable: it makes the boy more realistic. Shinji is actually the most level headed of all the characters. He doesn't buy into the completely insane situations and world, whereas the rest of the cast can't understand his lack of enthusiasm. Part of what makes it so uncomfortable to watch is just how close to home the satire gets. Even the bizarre religious imagery is a reference to the chaotic art design big mecha anime tends to have.
Sadly, no one got the joke. Some dismissed it, and some, perhaps more damaging to the creator, took it seriously.
The original ending was pitch perfect... it neatly portrayed the shoe horned in ethical message that nearly all anime has, including the often trippy sequences associated with final episodes. The only thing different they did was cut out the action sequences, leaving it more as an abstract evaluation of big mecha anime in general. That... really doesn't work with the general anime watching public. This is an audience that appreciates stability in story telling, with obvious checkpoints (beach party episode, hot springs episode etc... all of which Eva parodies in subtle ways). So a remake was made.
End of Evangelion can either be looked at as making the parody more obvious (which was unsuccessful), or as is more often interpreted, the creator literally ripping apart his own creation as an attack on the fans. It's all there. Watch it again, and bring with you a checklist of stuff you'd expect to see in a finale, and look for the twist on each one.
Neon Genesis Evangelion has depth... just not the kind of depth that everyone thinks it has.