well this is my logic and i posted it in jedi's thread but i will post it hear again, just for you...
when neo was in the tv room talking sh!t with the archi, the archi said that his "life was a sum of a remainder of an equation inherent to the programming of the matrix". which from my understanding is (1) the anomaly code was an accident (2) neo wasn't chosen but rather a casualty of the unsolvable equation. and like xeous said, the architect made his sincerest efforts to eliminate him in what is otherwise a harmony of mathematical precission.
which leads me to another theory that the oracle introduced that variable (the anomaly code) into the matrix without the archi knowing about it because her purpose is to unbalance the equation. and the archi created sentient programs to balance the equation.