Smith: The New Smith

In M2, two Smiths walk up to a dead Agent (or dead body used by an Agent) and have the following exchange:

Smith 1: “That went as expected.”
Smith 2: “Yes.”
Smith 1: “It’s happening exactly as before.”
Smith 2: “Well, not exactly.”

The lines "that went as expected" and "it's happening exactly as before" both refer to the fact that Neo (the One) effortlessly kills all of the Agents he fights. In every previous version of the Matrix, Agent Smith was always killed by Neo's predecessors every time they had an encounter.

But this time, Smith knows he finally has the potential to beat the One, because Smith is a virus who inherits all of the abilities of programs and humans he takes over. As the two Smiths look down at the beaten Agent, they are both thinking, "That was me dead on the ground so many times before. Now, I can finally beat the One." So, as the two Smiths point out, things are going exactly as before (Neo is very predictably slaughtering all Agents he encounters), but not exactly (Agent Smith will not be killed by the One this time).

In M3, when several Smiths corner Seraph and Sati, we see another indication that Smith is now more powerful than he was in previous versions of the Matrix:

Smith: Well, well, it's been a long time. I remember chasing you was like chasing a ghost.
Seraph: I have beaten you before.
Smith: That's true, but as you can see, things are a little different now.

First, Smith tells Seraph that it has been "a long time". This could refer to several decades, or it could refer to past versions of the Matrix (a century or more). Regardless, now that Smith has multiplied, Seraph stands no chance of beating Smith. This is further indication that this is the first time in Matrix history that Smith has been able to duplicate himself as a virus. He is a new Smith.

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