Wilt has great physical skills, but Jordan's greatness is beyond that. Jordan had the mental toughness to do what he does, night in and night out, and the results were that his team won night in and night out. For six, SIX, straight years, he dominated the league. The only other player coming close to that would be Bill Russell, but his offensive game is not at the same level as other great players. Sure, Jordan had help doing that, but so did Wilt(Jerry West, Elgin Baylor, etc.).
I have never seen Wilt play in person, but from what I have read, and the fact that Wilt was only able to win one Championship with a very good team, I think Jordan wins. And if you put Jordan in Wilt's time, I believe Jordan will make equally impressive impact on the game of basketball.