We are never going to know. It's really opened-ended. In the "open-ended endings" thread, I make a comment about there being a difference between trying to make an open-ended ending and just not telling the story write. EoE is really right on that line between the two. On the surface, it's nuts and nothing makes any sense. But at the same time, if you do research into Evangelion, it makes more sense. There is so much stuff that was vaguely hinted at, or not told at all in the anime that makes the series make more sense.