The series actually did not end the story, which basically finishes when the mass-produced Eva model shows up, controlled by the dummy (butt)plug, so basically there's no need for those whiny kids anymore.
It turns out that the reason for the angels' attack was that Shinji's father wanted to undo God's work by reuniting all humans souls into a unique being (giant Rei). God itself may be that giant Rei too.
However, being God comes at the price of loneliness. Shinji refuses this idea and becomes the new human Adam, and that german chick the new Eve. The rest of the world is devastated (the other half) and basically they're all that's left to rebuild the human race.
Now why does Shinji has all that power? Because he was born during the Second Impact, brought by finding the Angelic Adam (Adam Kadamon in the Kaballah) in the south pole. He's like Kaoru, who was an angel in human form.
Dunno, its pretty clear to me, granted its a crazy story but at least it has a definite ending. There may be a metaphor but I'm just taking things literraly as shown.
For a more interesting metaphor though, try to figure out the real meaning of FLCL. :)
[download a life]