As true PF, Malone was more versatile in the offense. He was always in the middle of the fast breaks (rather than trailing), and he was a great finisher to the rim. He developed an excellent mid-range jumper. He was an all time great rebounder. He muscled his way into low post points, but he was not a true post player. If I were to design the perfect power foward it would be Malone.
Duncan was a center with a nice shooting touch. If I were to design the perfect starting five, I would rather have Malone playing alongside Kareem or Wilt than Duncan. A lot of what Duncan does would be duplicative of what Wilt or Kareem already do. With Duncan playing alongside Kareem (rather than Malone), my transition game would suffer, and I would become more dependant on half court sets. Malone gets me a lot more flexibility on offense and would allow me to instantly switch between an up tempo and half court game.