Okay, why would Neo really return as the Oracle said? Trinity is dead, and he has no reason to come back. He has completed his task on earth. And what about the machines? Clearly, they don't want another war due to too great losses. It was Neo's (see "Jesus") deal with the machines, to end the war if he could defeat Smith. He was like his own religion to everybody, and everyone believed in him in the end.

About Neo's EMP, I believe it was answered in the movie. He had a connection with the source after visiting the creator in Reloaded, so he could blow things up in the machine world as well, knowing they weren't truly real either. What isn't real can be controlled.

"Stephen Wolfram is the creator of Mathematica and is widely regarded as the most important innovator in scientific and technical computing today." - Stephen Wolfram