Agent smiths differ from the other Agents

[cloudwolf]

It's a good point. If Smith was a planned part of the The One cycle (i.e. he was a completely natural bi-product) then what made it get powerful enough this time around to threaten the Machines and give Neo something to bargain with?

The key difference in all of this is Trinity. Thats where the cycle broke. The moment the situation was allowed to go past the point of reset Smith became too powerful to stop. Neo and Trinity coming together was The Oracle's doing.