it seems to me the reason that neo's powers transfered have everything to do with his decomposition of agent smith at the end of the first movie. smith and neo were both fundamentally changed as a result, because they had absorbed parts of one another, become linked in some strange fashion, whatever. by absorbing part of a machine, neo gained the ability to translate some of his messiah powers into the real world, although at a terrible cost to his body. smith became able to exist in the real world because he had part of a real person in him.

the more important thing is, neo and, just as importantly, smith are wild cards THAT THE ARCHITECHT HAD NOT FORESEEN, that exist outside the bounds of his perfect logic, that his logic cannot account for. Get ready for that to be the theme of Revolutions--how these two wild cards bring down the Matrix (and not by teaming up--that'd be way too easy).