Agent smiths differ from the other Agents

[Metalogic]

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.

I believe so. In Revolutions, Seraph made a comment that he has beaten Smith before.

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When the Oracle said that the Architect balances the equations that always led me to believe that the Architect had written Smith a little differently than the other Agents. Smith was the Architect's answer to Neo. "The equation trying to balance itself out."

Maybe Smith was selected because of his hatred for humans.

I'd modify this a bit. Smith was chosen, but I don't think The Architect's chose him directly. From The Matrix to Revolutions, Smith and Neo were always equal. Remember, in Reloaded The Architect said this:

Precisely. As you are undoubtedly gathering, the anomaly's systemic, creating fluctuations in even the most simplistic equations.

It's just in the coding of The Matrix, when Neo arrived and started to become The One, Smith started to become more self aware. Hence the system trying to balance the equation.