I preferred an alternative explanation, where The One actually comes in two parts, a program in the matrix, and a human in the real world with a direct neuro link to that program. Neo's powers are expressed in the real world because he still has a direct link to the machines.
http://www.cyberpunkreview.com/movie/essays/understanding-th...
I liked the sequels a lot better once I read that. They're still not genius cinema, but they're better.