remember what the train man said about that station of his, "down here, I'm god"? there are forces more powerful than Neo in the world of the Matrix; neo can't change things he doesn't have the proverbial access codes to. And assuming Agent Smith's code combined with that of the virtual Neo in the end of the first Matrix, it would be assumable that Smith then has the same powers as Neo does. I think the final scene, of the sunrise within the Matrix, was a little corny. They should have shown a preview for the Animatrix Part 2, where humanity deals with getting back to the surface and freeing the humans who want out of the Matrix. yeah, they need an Animatrix part 2.