Was the Matrix Hero Neo a manifest of belief and created by a few or an enigma of human genome that has superior intellect even to A.I.?

I thought of it as a person who was able to go outside the code. The machines are all running on code. They all have their restrictions based on their own code. Neo was able to rewrite the code. The rest of this thought would be drawing from 2 and 3 though. They basically show it as an expected anomaly that would show up. So they built the Matrix around that expected anomaly. Allowing for it to happen, then reset the system and start again. Machines are unable to fully understand human emotions. They consider it irrational. I think that lack of understanding made it impossible for them to make the Matrix truly bug free. Neo is a bug in the code. But one they accounted for. So they simply applied a system reset whenever the bug presented itself. Then the Matrix would run fine for a while again. Agent Smith mentions that Neo had passed his abilities to edit the code onto him (when Neo combines his code with Agent Smith and then obliterates him). So the bug can be passed to other programs. Kind of confirming Agent Smith's theory that humans are a virus.