i'm just thinking about it from a coders view. just like the architect said they were getting exceedingly efficient at destroying zion, they could also get exceedingly better at writing the code of the matrix. he said he counted versions of the matrix from one emergence of an anomaly (neo) to the next. so i see it as everytime a neo came, the matrix was rewritten. maybe it was just in the past, because the first 5 neos went back to the source to do whatever they were supposed to do, and this neo didn't. but i've written a couple of programs, and rewritten them a few times, and each time i rewrote them, they got better. did the same thing, just with less flaws.

cliff notes. i agree that there is a flaw, and that flaw causes neo. but i'm also saying it's possible (maybe not probable) to get rid of the flaw while still maintaining the function of the matrix.