Still more spoliers

It could be that he *thinks* he's left the Matrix but hasn't really which would nicely explain away why he can do the funky lightning stuff

The best explanation for everything that I can think of so far (though I don't think it's true) is this:

For the Matrix to function there must be choice. Therefore everyone is given a choice of the Matrix or Zion both of which are simulations. Zion is for the 1% of people who reject the Matrix and need another place to go. However, there is still another 1% who will reject the Zion program. When these people appear as they necessarily must they become the "one" and the whole system is rebooted. It's all a cycle to control humans, but now Neo is breaking it by choosing love over destiny. Like I said, though this is the best explination I have so far I'm betting (hoping?) we all get suprised in the last movie.

The one thing that seems clear, however, is that even in the future the NT code base has survived, and in fact been used to develop the Matrix, hence the need for systematic rebooting.