Gah, you guys are sitting here talking about the true meaning of Eva and crap, and I read and I've never even seen EVA.
What a good way to ruin the story for myself, huh?
I'm sorry, but "Shinji did/didn't choose instrumentality" has to be the most un-spoilerish giveaway I've ever seen, especially considering that the whole thing only makes sense in retrospect.
Anyway, I think it's obvious how they could do an Eva sequel. See, it turns out that the Angels aren't really apocalyptic forebearers, but terribly misunderstood aliens from a far off realm of space, and a new batch of Eva pilots have to hunt each one of them down and collect them in order to power-up for the upcoming battle with the Decepticons....

Als Gregor Samsa eines Morgens aus unruhigen Träumen erwachte, fand er sich in seinem Bett zu einem ungeheueren Ungeziefer verwandelt.