Ok here's my take:

At the end, the little Indian girl asks, "Will we see Neo again?" and the Oracle says, "I believe so" or something along those lines.

Why?

Because WE ALL JUST GOT ****ED.

I think that that "end" is what happened with the last 5 versions of the Matrix. So what if humans and machines live in peace? The machines at any time could **** up all the humans and start over.