I have become increasingly convinced that a matrix within the matrix is the only way to explain most of the questions raised by Reloaded. I think there are still quite a few supprises in store however for the final movie. Just from watching the previews at the end of the second one's credits there is hints that Smith is making a power play to take over the matrix (or something) and that the only way to save humanity is for Neo to once and for all defeat Smith.
