I'm not really clear on why the cycle is supposed to be important to the machines. It has something to do with them using the free will of the One to help reprogram the matrix, by forcing him to make a choice (save Zion or save Trinity). The machines apparently have no free will of their own, so they must use a human for this ingredient.
I always thought the point of reprogramming the matrix was for the architect to try and iron out the flaws, the flaw being the anomaly that results in the one.... Actually thinking about it the architect said the first matrix was perfect and it was rejected, choice was the key to its success but it created the anomaly... So is he trying to rid the matrix of the systemic anomaly and keep choice or is he... no im just lost now, i need to watch it again.

I love the animatrix, the haunted house was probably my favourite but they're all good.