Something that had occured to me during the movie that may be a possibility.

Neo is version 6 of the One coding and is used much like the Oracle is. Control over people by use of a myth or a legend that they believe to be true.

As for the early portion where he had no plugs I also noticed that and commented on it to a friend of mine then he pointed to the screen and I thought it was just an obscured view.

I came up with the matrix in a matrix idea at the end of the movie when he disabled the sentinel but I don't know about that theory holding much water.