Malone was a PF when there were better centers. But he never played center. Duncan played PF in a time when there were better PFs than Malone played against (Dirk/Webber/Garnett.)
Malone scored a lot. No doubt.
His defense was largely made fun of by his peers because it was mainly hacking at wrists. In the 92 Olympics, Jordan and Magic made a skit about it during a practice. Meanwhile, Duncan has been All-Defense more than any other player that ever lived. Duncan has been All-Defense as many times as Michael Jordan and LeBron James combined.
Malone shouldn't have won either of his MVPs. One over Jordan, one because the vote was split three ways and he was easily the least deserving of the three (Simmons went into both of those in his book.)
Case for Duncan is much stronger. Including the fact that Duncan has back to back MVPs, four rings and three Finals MVPs. He is also 11 spots higher than Malone in the Simmons HOF Pyramid.
http://www.basketball-reference.com/awards/simmons_pyramid.html LeBron has won two rings since Simmons updated that, so Malone will likely be lower next time Simmons updates.
Again, all you really have is longevity and scoring. Malone was a worse rebounder, worse defender, worse shot blocker (didn't even average 1 per game) and was never a winner. Plus what really matters: Duncan has scored more points in the playoffs than Malone, despite quite a few less seasons. Duncan has more rebounds in the playoffs. Duncan has more assists in the playoffs. Duncan has the most blocks in the playoffs all time - 400 more than Karl. Duncan has more blocks.
Oh yeah, probably has something to do with the fact that Karl Malone only got the Jazz to the Conference Finals 5 times and lost in the 1st round 9 times, despite playing with two top-30 players of all time and a HOF coach. Meanwhile, Duncan has made it to at least the Conference Finals 9 times, has four rings and was the best player on every Championship team he was on. Oh yeah, and Duncan only lost in the first round twice.
So if you value winning and playoff performances, there is no question Duncan is the better player. If you value scoring a lot of points over 20 years, go ahead and pick Malone.