Japanese-with-English subtitles is the ONLY right way to watch it - the English dub (atleast on the version I saw) was pretty cruddy.
I think it's pretty truthful that original-audio-with-subtitles is the only way to watch something made in a different language. I suppose it's possible for dubbers to recapture the original emotions for the audio, but it's a rare thing.
But yeah, NGE is pretty darn cool, although you get the feeling that the maker wasn't sure what kind of movie he wanted to make. It moved from giant-robo saga to political drama to sitcom to mindfuck in the space of 26 episodes. Incidentally, if you want a real headtrip on the concept, check out Children of an Elder God, a bit of fanfiction looking at what the world of of NGE might have been like if the mythos were based on Lovecraft rather than Judeochristianity.