SirMystiq has it down pretty good. From a long discussion with a friend of mine, we came to the following conclusions:
In mathematical programming, a continuous anomaly looping over and over again will, at one point, cause an entire program to come crashing down. If that\'s the case, then the program needs to be restarted and the anomaly needs to be weeded out either through careful scrutinzation of the problem, or trial and error. If you think of the Matrix, both the real form of the Matrix represented by Zion, and the form of the Matrix represented by 1999 life, as a series of mathematical equations equalling a program, Neo is the anomaly in that equation unsolved by the machines, the human anomaly of choice.
The machines are attempting to contain that anomaly and phase it out of their program as best as they can by giving the humans a choice at a very limited concious level. One of those humans will be an anomaly and be dubbed as the one, or the 0.1% that the Architect spoke of. Their ultimate goal with the one is to recombine them with the Source and restart the system since the mere existance of the one, and others who chose Zion like him, are further proof that their equations have yet to be perfected. Since this is a continuing struggle for the machines, the system needs to be continually restarted every hundred years until the equation is perfect and accepted by every single human and thus, there would be no need for Zion and control would be ultimately supreme.
With that said, new variables are introduced to the One in order to properly phase them out of their existance leading to the complete control of the Matrix with the machines and the variable of free will would be moot. Thus, the machines, or even the programs of the Matrix, introduced Trinity. As they said in the film, the One had never really been given a true element for them to really attach to. They were always sympathetic enough to humanity to cause them to save the vast majority -- the needs of the many outweigh the needs of the few, or the one -- but that has yet to phase out the variable of the One. As said in the beginning of this long winded explanation, new elements are introduced to get rid of the One and because of that, the element of love was introduced, something the machines do not fully understand. Either way, the machines risk losing the power source of the humans either through a total system failure of the Matrix through the anomalyous program loop, however, the machines can continually try new concepts to try and perfect the Matrix program code. Either way, it\'s a risk, but it\'s a risk worth taking.
