»My Question..«

Why would the machines allow neo and the humans 2 live after neo killed smith and desposed of there problem for them (the equation is now blanced out) , why after all these years of fighting when the machines can final destroy the rebelion for good and kill neo and win the war would they decare peace?
Smith was destroyed and wheather or not Neo died or not they could easyliy kill him in the Machine city, why dont they wipe out Zion and kill all the free humans so thered be no one left, reboot the matrix and thereve one the War there been fighting all this time, why suddenly would the Machines make a deal for peace we they have basically won?

Quote:

The Architect: "As I was saying, she stumbled upon a solution whereby nearly 99.9% of all test subjects accepted the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level. While this answer functioned, it was obviously fundamentally flawed, thus creating the otherwise contradictory systemic anomaly, that if left unchecked might threaten the system itself. Ergo, those that refused the program, while a minority, if unchecked, would constitute an escalating probability of disaster." Neo: "This is about Zion."

Maybe because the machines knew it would be inevitable that humans would free themselves and create another Zion? its all about balance again, you need both worlds for balance.

The machines have only won when theres balance. Also balance cant happen with just the matrix alone, and the next "One" cant develop into a super-being without Zions existance. They need Zion to groom the next One so they can wipe out any future threats like the Smith virus.

this is my guess.