Ground rules: Of course Wonder Woman could clean up with Neo in the real world, so we are going to place her with all her Amazonian abilities into the Matrix for this fight. Digital Diana may seem like a stretch, but it's only fair. See my post on home court advantage for details. As far as Neo goes, his power levels reflect those shown in the Matrix Revolutions.
Personal Bias: I loved the first Matrix movie and I like the other two films a lot more than most. If this was a popularity contest, Neo FTW.
Fight! The combatants charge each other immediately, both expecting an easy win. Each blow is blocked or dodged at speeds barely perceptible by a human eye. Neo didn't realize that Wonder Woman is a warrior with extensive training with some of the best fighters in the world, in that aspect she is more like Batman than Superman. However, the fact that Neo has uploaded all the moves and techniques of every major fighting style and martial art still gives him an edge. He eventually connects, knocking Diana down clean though the cement of the street and into the sewers below.
Before Neo can inspect the sewer, Diana ...