As a San Antonian, I am unashamedly biased towards Duncan. However, I have great respect for Garnett.
Personally, I think the difference between the two, and what makes Duncan the better player, is teamwork. One man does not a team make, which Garnett learned with the TWolves, James learned with the Cavs, and this year the Lakers learned when they discovered that their team was shallow (oh, the irony).
Initially, Duncan had Robinson. By the time Duncan was a leader for the Spurs, he had Ginobili and Parker. Along the way was a laundry list of players who could come off the bench and make something happen on the court. And Pop was, and is, always there (and usually angry!).
Maybe Garnett should have gone to college and grown up a little more before joining the NBA. Maybe he just got unlucky and was a young guy who bought his own hype. Despite getting a ring (which I'm glad he has because I think he more than deserves it), I think there's some wasted potential in Garnett. When Duncan's finished, he can know that he left everything on the court.