It all depends on the team, the system, and the personnel on that team. Right now, what teams with their current rosters would take Dirk over Duncan?
Miami - Dirk complements Shaq better
Houston - with T-Mac and Yao, Dirk is a better fit
Cleveland - high-low action with Zydrunas
Phoenix - style and tempo is better fit with Dirk
Indiana - Dirk and Jermaine would probably be a better inside-out duo
Denver - Camby already downlow, Nuggets need outside shooting and have an uptempo style
Seattle - uptempo, 3-point shooting team
Memphis - Gasol an inside force, Dirk fits better
Orlando - Dwight Howard is the low post threat
Charlotte - Okafor and May already inside presences
New York - Eddy Curry needs space down low
maybe New Jersey - uptempo style, toss-up between the two
maybe Sacramento - toss-up between the two
maybe Milwaukee - toss-up, Bogut as the center, Dirk the high post PF
maybe New Orleans - I think that team would like either, but Chris Paul might like playing with Dirk more