I've made it through the entire original run this week, and I've got 2 more episodes of End of Evangelion to go before that one is done.
I'm finding myself much preferring the EoE version of the ending - it was nice to see character's plots being tied up visually, and it just kind of....made more sense to me.
I know there's another series of NGE (Rebirth, right?), but I might only watch the parts that expand on the story.
The cool thing about Evangelion is that you don't have to choose a favorite. It's a very rare opportunity to see how a single story can be told in different ways for different times and different meanings. All of the endings are good, in my opinion.
Personally, I don't think the original ending is in line with the pessimistic tones of the original run. I find it kind of strange that shinji self actualizes at the end when there's really no indication as to why that would happen. Because of this, I think EoE caps off the the original run perfectly.
However, Rebuild presents a very different set of events, and the optimistic self actualization ending makes a lot of sense. It decided to retroactively make the original ending appropriate.
So... They're all great