»a melding of two theories........«

Okay, this is a stretch and I'm a newcomer, so I'm on dangerous ground....
If Zion is MWM, then it would be plausible to suggest that neo is a program. Say neo is a program like mero, oracle, or keymaker but a program still in use by the system, not an exile. Let's also say that zion is MWM, unplugging neo would be a matter of downloading neo's files from one matrix to another OR neo's files being moved to another location or higher up (from 2003 matrix to zion matrix) in the matrix. "another system of control" neo says.

Disclaimer: I don't really believe in either theories. I just thought it would be fun to explore.