I've always thought that Zion was a catch basin for those who couldn't accept the main Matrix program.
After all, it presents the perfect scenario for skeptics and conspiracy theorists: a future in which they are persecuted and manipulated, with a clear enemy to fight against.
That would distract them seeking out the ultimate truth: that they still have not emerged into The Real.
This theory was pretty wide spread, apparently.
It makes so much sense to me, I was convinced it was the case.
Yet, if it were actually a thing, the Wachowski's would have put in a nod to it in the latest film.
They did not.
So much for my movie interpretation skills!