How about the guy who kidnapped the Keymaker? Who and what is his nature? My guess is that he used to be Neo. Rather, that guy is Neo #6. After the start of the new Zion, Neo as a program/human became dispensable. So, he became an exile. He no longer needed to be superman. In his boredom however, Neo#6 became corrupt and started writing code that got him some nookie in the women's restroom. The henchmen of Neo#6 were in turn the other partners of Neo #6 or were the other exiles/computer programs who were chasing Neo #6.