Zion is, indeed, inside a Matrix, and the Matrix we know and love is, indeed, a submatrix. However, Neo's a program - as is everyone we've seen so far in the movie. And the Matrix is built by humans, not AIs.
So what's Neo?
He's an attempt to get a full working AI. One of the tests for a "real AI" is whether it can love. Which he has passed. So, the plotline for Matrix Revolutions: Neo passes the rest of the AI tests, and is informed "hey, guess what - You're an AI! We're all humans! Your life was a lie. Now work for us!"
Neo gets mad, plots revenge. Orchestrates robot takeover in the *real* world.
Wouldn't that be ironic? ;)
