I'll have to
contradict this. Smith is not the One. The trick is the main computer system is hooked correctly into Neo at the end so when Smith takes over, the system has a direct line to him and can delete him.
That could totally be what happened.
And it would be as better movie too.
except it is explained that the reason the "one" is so dangerous is if he/she/it is downloaded into the source or main computer or whatever then it will reeset the matrix and it furter is explained that the Oracle created the one and the reset glitch.
Thats why she was the only one who could identify him and Remerber the end the dude coming to the Orical like well you finally did it.
Which would mean the "one" is a program logically. It is also said the "one" can change the matrix to his will. Neo bent the rules but never just completly changed anything . Smith on the other hand changed people into the matrix into him plus completly changed his surroundings in the last fight. He even ask Neo "do you like wehat I've done with the place" and a quick look around looks like a video game fighting background , no shops or doors just big generic buildings . the first hint is Smith calling the Oracle mom .
So if neo is the one he would have reset the matrix immediately including Smith's programming but he wasn't so he couldn't and he didn't. Smith did.
Neo just realized more than anyone the matrix is in your head so you can control your actions as long as it does not go outside of the structure of the matrix . which anyone in the matrix could do if they believed enough . meaning everyone in the matrix fights up to what they think there ability is .
Neo was told he was god like so he became that.
I would say this is my opinion but they flat out explain it in the movie . the problem is they explained EVERYTHING and it was so complicated and you only get pieces here and there and not in the right order .
Besides what did the Oracle tell neo when he asked if he was the " one" in the first movie ?
See it took multiple paragraph to just scratch the surface of explanations .