I think code really improved X-Men. They added combo awards, Deadpool, Nightcrawler activity, wizard modes, multiball scoring changes, and made the game much more about strategy and VERY accurate shooting.
When the game first came out, the rules were bare bones, and the shots did not seem to have much cohesion, and there was not much strategy other than start Wolverine and Magneto. Code improved that and its now one of the more challenging and fun games of recent years (IMO of course)