The idea that someone PUT Smith in the Matrix is a bit far-fetched, to put it politely. We’ve run into plenty of the machine AI’s that act with as much jaded emotions as an audience at the latest Ohrah Winfrey, so an AI going nuts at the endless repetition, doesn’t prove Smith was originally anything but an agent.
Smith just HAPPENS to be the agent that Neo, having assimilated the anomaly, is capable of deleting. This deletion, this use of the anomaly that causes fluctuations in the simplest of programs, may be the key to the system-crash of the Matrix. Not Smith in and off himself.
Perhaps the mere anomaly is what end causing havoc in the virtual reality. In this case it’s part of it having inserted itself in the Smith-program, so he doesn’t have to return to the Source.
The idea about the math (viz a viz 1 divided by 3) is interesting. However, the Architect explains that the anomaly is due to an unequal equation (pure math nonsense). Even we, humans, cannot write out 1/3, that doesn’t cause any anomalies in our existence. The anomaly is caused by the paradox of having to give humans choice. The problem of free will, which is alien to the machines (seen in the purpose-search of Smith). The Matrix only works as long a humans accept being plugged in, even if it’s only on a near unconcious level. But they are not given a choice.
Too much of it has already been discussed here already and is not novel in any way. The Merovingian as the first One (of Matrix 2.1) is ludicrous, in as much as the One chooses 23 people from the Matrix and rebuilds Zion and dies there. The postulates that Morpheus and Trinity are programs are just that – postulates – without any proof or arguments to support the assertion. That is getting a little tiring, reading hypothesis after hypothesis with no arguments to support them. And they idea that Trinity must FORCE the One to fall in love with her so she can BEAR the next one is complete idiocy. And usually shows a peculiar and Victorian approach to sex, as in sex is only allowed to procreate the species.