Here's my theory: The Architect and, hence, the machine world accounted for everything that happened to Neo right up until he made the choice to go after Trinity instead of accept the Architect's stated terms for the survival of humanity. The machines can't conceive of or predict that Neo would make the choice he makes--their strictly utilitarian logic leaves no room for Neo's making a decision that places the entire species at risk for the sake of one woman who (they feel) is going to die anyway. They can't factor love into their equations, in other words.

So, by making that decision, Neo has become something their logic can't predict. For the first time, including the first five Chosen Ones, a human has done something outside of the grand design of the Matrix. That calls off every plan the machines made, throws a wrench in every scheme they have. Put it this way: if Neo doesn't now represent a new, fundamental challenge to their order, something unprecedented and frightening, why are they willing to destroy the entire human race and "accept a lower level of existence" for themselves? Neo's a wild card, something they couldn't predict or control, just like Smith.

As for his real world powers, I kind of hope it's not the "anothe level of the Matrix" story. I trust the brothers to come up with a good reason why Neo was able to do what he did without resorting to the "world pulled over the world pulled over the world pulled over your eyes" thing. I think the bond between Smith and Neo is obviously key to everything that happened in Revolutions, so I have to believe that the link between the two of them, having been so developped, matters in a way that is fundamental to the resolution of the story.