When I ask myself who would win in a fight, Neo or John Murdock, I side with Murdock. As powerful as Neo is when he's in the Matrix, he pales in comparison to Murdock's matter materialization. When Neo becomes Jesus, Murdock becomes God. I know, that's a dumb way to assess which movie is better.
Really though, where the matrix hits you with the bombshell discovery early, Dark City takes you for a long ride with a satisfying end. Basically why I liked it. Also, the possibilities for a sequel is far more interesting than the sequels we got from the Matrix.