for one thing, no one could hav gotten to the machine city without being blown to pieces by those bombs except for Neo. He is the only one that could hav gotten that far. Then it all comes down to the purpose of a program and a person. Smith is a virus, and a viruses purpose on this ocassion is to take up everything in its path, but there is no area for it to go unless it would be to cross worlds. That would mean that Neo is the anti-virus. His purpose is to flush out the virus. Since smith already knew a part of his denstiny, he had a little problem letting go of reality, because he knew what would happen if he took over Neo. That's why he was telling Neo "Get away from me." Neo had no reason to live also, for he had lost his love, and he didnt really care if he died or not.🙁