My Opinions of the Matrix Universe - SPOILERS!!!
I think the machines wanted peace all along. I think that the 5 ones before Neo, the ones that entered the source allowing a dissemenation of the code they carried reinserting the prime program (what happened at the end of revo) were not supposed to do that. Since he was trapped in limbo, he kept having visions of the machine city and only after that he KNEW what he had to do. Not go there to destroy it, but to strike a peace. I think the machines, in the GRAND SCHEME of all things, purposly created smith (Neo's opposite, in other words, the equation to cancel him out) to see if neo cared enough to save BOTH their worlds. And when he made the deal with the huge talkin machine, I have to believe that since they didnt just slaughter him right then and there that they too were wanting peace all along. Think about it, two enemys hate each other (man n machine). They waste years fighting each other for nothing, but a greater threat comes(smith) and the two must unite probably for the first time EVER.
Once neo figured out what he had to allow smith to do in order to end it all, he did it because he chose to. He gave his life for the future of both worlds and I think the machines were waiting for that, since they very gently carried away his body instead of just tossing it aside. They machines in the end, served their purpose to serve man.