[FS]

My idea is, the Matrix might've been made so complex that it works like an overly bureaucratic system. One program answers to another and another and another. They have been written to be allowed a certain number of actions, but can't move outside of those. Otherwise agents, for instance, could just instantly kill anyone in the Matrix posing a problem. This could be tracked down to the highest programs, the ones that control everything, and for that purpose are as primitive yet efficient as insects. They would write programs complex enough to function inside the Matrix, but not complex enough to act independantly.