My theory?

Like Sykin says, Neo (aka The One) is not actually the anomoly (the anomoly simply being the mathmatical percentage) but instead the pyhsical, and ineviatable, manifestation of it. The upgraded agents simply refer to him as the anomoly because well... its easier to say than 'the natural occurance diritive from the anomoly'. This theroy fits with the Architect's dialogue too.

As for Smith, he was an agent to begin with, nothing more. Well, maybe a bit crazy but hey. Until Neo was reborn and The One code awakened Smith was just another program. But when The One was activated a natural counterbalance had to occur, this counterbalance code was released the moment Neo was reborn as The One. Ity then began to search for a host. Since Smith was the first thing Neo killed, causing his his code to scatter all over the place it chose him. Since he was an easy target. 

This infection was what led smith to deny his programming to return to the source. Instead, he became Neo's opposite. But only after Neo's awakening. This would explain why the Architect didn't delete Smith beforehand. Because he simply didn't know he'd be the counterbalance.

From there on out the pre-planned scenario played out, The Machines were sent to destroy Zion and the 2 opposites played their parts inside the simulation. Now, this normally cumulates to the re-insertion of the prime program when the Architect meets The One. Giving him the choice between a reset or the complete destruction of the human race.

But this time The One choose not to return to the source. This threw all the Architect's plans out of whack, the opposite's existance past the re-insertion point was never planned before. Smith grew past The Machine's control. This is why Deus Ex Machina agreed to the truce.

And the rest they say is history in the making.

So...

The problem is choice
Neo is the anomaly and the integral anomaly.
Smith was/is Neo's equal and opposite reaction.

RainKingX wrote:

So...

The problem is choice
Neo is the anomaly and the integral anomaly.
Smith was/is Neo's equal and opposite reaction.

Which Is why IF Neo was some type of Arc or Oracle created Hotfix it was for the problem of zion NOT to Patch Smith. The other point being that otherwise the Architect could have deleted smith at least before Neo bugged Smith, if not before theSmith Virus takes on the Oracles RSI.

The Anomaly Problem 

Woah. In writing my first response to this, I was all prepared to argue that Neo was the anomaly. Mostly because of the Agents referring to him as such. After pouring over the Architect's speech during their meeting however, I realize that this is not the truth. Neo is not the systemic anomaly that the architect refers to.

The anomaly is what happens when a human becomes aware of the Matrix.

The Machines control the humans (bluepills) in the Matrix, by making them aware of the fact that they are part of the simulation. The only way they can do this with 99% acceptance is to give us a choice on a "nearly unconcious level": choose the Matrix, or reject it. Those who reject it, become aware of the simulation and become Awakened (redpills). These Awakened represent the 1% who cannot accept the Matrix or be controlled by the Machines. The Architect says that if these Awakened were left unchecked, they "would constitute an escalating probability of disaster." That is when Neo realizes exactly "why" he is supposed to save the human race.

The One is how the Machines control the 1%.

Using a Prophecy passed down by the 5th One at the beginning of the sixth cycle of the One, the Machines have put the freed humans on a path to follow this prophecy until the "return" of the One. And so, the humans wait, hoping for the day when the One returns to save humanity. This benefits the Machines, because the humans don't get it in their heads to start tearing apart the Matrix or take on kamikaze missions to take out the battery city with hovercraft, or resort to other crazy unpredictable behavior. All they have to do is wait and watch for their savior.

Then, when the Machines deem Zion to have become "full", they create the One (a thirty-forty year process, because Neo is "irrevocably human" and begin the process of destroying Zion.

Maybe the upgraded Agents refer to Neo as "the anomaly" because he is an Awakened, and therefore an anomaly. Maybe he was "the" anomaly they were sent to find.

I would also venture to say that the scenario of a savior would appeal most to humans, making it the most readily accepted form of control the Machines could use.

***

The Smith Problem 

Neo did not become the One until he died. During this critical process, he realized the extent to which he could control the Matrix. After this pivotal moment, his awareness of the Matrix was heightened immensely. Until Neo overwrote the Smith program, the Agent was just that: a program. When Neo overwrote him, a connection was created between Neo and Smith, whereby Smith gained Neo's heightened awareness of the Matrix. Every time Neo's powers progressed, so did Smith's.

In short, Smith was an accident, created by the One. That's why he was beyond the control of the Machines.

***

D@mn , I wish I could make a living at this. Right or wrong, it's a lot of fun. . .

The Anomaly Problem 

Woah. In writing my first response to this, I was all prepared to argue that Neo was the anomaly. Mostly because of the Agents referring to him as such. After pouring over the Architect's speech during their meeting however, I realize that this is not the truth. Neo is not the systemic anomaly that the architect refers to.

But if all awakened humans are anomalys... then Neo would be the root of the problem because he freed thousands people in the six months between The Matrix 1 and Reloaded.

So he would be the anomaly that is at the root of the other anomalys....

Well, it's not thousands, exactly. Morpheus only says that "in the past 6 months, we have freed more minds than in the past 6 years". While this number is probably substantial, considering the big deal they seemed to make of it, it probably wasn't thousands.

And they never really say how proactive their 'recruiting' process was. Perhaps the anomaly was occuring at an accelerated rate. This may have been the catalyst that the Machines used to identify the time to initiate the actual attack.

You're on the right track, though. Keep it coming!