Agent smiths differ from the other Agents

[QuiDormit]

I think programs are able to develop and become more self aware. If Smith was an Agent in the previous cycle, then maybe over time he was able to expand his programming like an exile expands their. When a program becomes an exile, they are no longer constricted by the machines programming. Maybe that's what happened to Smith, he became a quasi-exile. Maybe that's why he was chosen to balance out Neo.

Yet another system of control.