Agent Smith assimilates every person and program in the Matrix, much like a virus which he compares humans to in the first film. This assimilation leaves zero diversity, choice or freedom for all humans and programs in the Matrix. Effectively everything has become zeroized. This is "inevitable" as all systems will eventually breakdown. Neo is the exact opposite of this "zero effect"; he is the One, the balance. One and Zero. Binary code. .
The Architect oversees that this balance is achieved by allowing the Oracle to set the entire process in motion in order to reboot and upgrade the Matrix. Sati is no more than the last program thrown into the bitbucket before the big upgrade. Her only necessity is that she also needs an upgrade and she's the last exile program added to the syntax that is designated for an upgrade. Not all of the neccessary programs were in the Syntax when Smith tried to assimilate Neo in the second film which is why the reboot didn't take place then. Sati was the last required program in the Matrix before the reboot/upgrade could occur. .
When the Zero and One are balanced, the Matrix reboot can occur and all anomalies are removed and order is restored. Just like any system, periodic reboots are necessary to restore system integrity. Neo is coded to be this balance by the Oracle in order to achieve system integrity. By having this code within him, he is the bridge between human and machine consciousness. This is why he can feel the Sentinels and why he ends up in the train station even though he's unplugged from the Matrix. After manipulating the Sentinels in the real world, his confused consciousness ends up in the limbo between the Source and the Matrix. .
Zion has been destroyed 5 times before because the machines destroy Zion each time they are threatened. Zion obviously has started 5 wars but the machines do not erradicate humanity, they only stop humans from continuing as a threat.