Agent smiths differ from the other Agents

[Broker]

It always seemed to me that Smith was "leader" of the agents, so maybe he was a better program, or maybe an older program. In the beginning of "Reloaded" he makes the comment that it's all happening like it did before (or something to that effect) and he talks about the first version of the Matrix when he's interrogating Morpheus. All of which lead me to believe he's lived through some, if not all, of the previous iterations of the Matrix.