i think that part of neo became implanted into smith at the end of the first movie, and the other way around. at the very end of reloaded, we see the hacker that smith had taken over, the guy with the goatee. he's the only survivor of the counter offense that failed because of a premature emp blast. obviously smith was the one to set it off, buy why didn't he die with all of the others? and more importantly, why was he unconscious just as neo was?
also, if you've seen the trailer to revolutions at the end of reloaded, there is a HUGE showdown between neo and the original smith...it seems to be the most signifigant point of the movie
Also did anyone notice in the Trailer for part 2, that Not ONLY was Hundreds of Smith's Lined up in the Streets, but there must have been MILLIONS of Smith's....BECAUSE you can EVEN seen his copies standing in EVERY WINDOW in the skyscrapers in the Background of the scene.
So who ever said, he'd Populate the Earth or every slave in the Matrix as himself...You may be right.
Lets jump to the Next step. If Smith can inhabit someones physical Body, Im Betting that if he ACTUALLY WAS TO COPY HIMSELF ONTO EVERY SLAVE, inhabiting the Matrix, that Regardless if the Matrix was Destroyed, his abilities, would STILL be able sustain the lives of the people He joined with.
Sort of like how he did with Bane, but in this case, he'd save the world.