The Matrix Online Server Emulator

Touche, Meta.

You make an excellent point, I forgot about the Prime Program.

The Architect: The function of the One is now to return to the source, allowing a temporary dissemination of the code you carry, reinserting the prime program. After which you will be required to select from the matrix 23 individuals, 16 female, 7 male, to rebuild Zion. Failure to comply with this process will result in a cataclysmic system crash killing everyone connected to the matrix, which coupled with the extermination of Zion will ultimately result in the extinction of the entire human race.

However, it doesn't say if Neo is the Prime Program or if he simply carries it.

I think the software/ programming/ code Neo held was a "piece" of the Source. Mainly because the Architect's line "Your primary function is to return to the Source allowing a temporary dissemination of the code you carry, reinserting the prime program."

Maybe a reboot code, maybe an anti-virus. I'm inclined to think reboot. The architect mentioned a cataclysmic system crash, but that didn't happen after Neo chose wrong. It may have happened if Smith were to gain more power.

Only the Brothers know what the terms were for Neo's predecessors. I think we all assume it was the same, but if the above is true about Smith causing the crash, then the system crash may not have been a factor for Neo 1-5. For example, "Failure to comply will result in us being very angry with you and we will write you a letter telling you how angry we are, then ultimately kill you in the Real along with Zion and have to make another "One" without a reboot."

I'm not sure if it was the Wachowskis or other commentators on the films that said as the trilogy went on Neo became more Machine and Smith became more Human.

Well, I think the Cataclysmic System Crash (CSC cause I'm lazy) was a threat that's supposed to make the anomaly feel an emotional outreach to his human counterparts.

The system may have crashed (eventually - the Architect never said that it would be immediate, he said that it would lead to a CSC), but Neo's ace in the hole was the Smith virus, which the Oracle concocted. Without the Smith virus, Neo wouldn't have had any sort of negotiating power with the Deus Ex Machina. They probably would have just killed his ass (or forcefully plugged him in) if he showed up on their doorstep and took what they wanted in some way or another.