Shaq was more dominant than Duncan on offense simply because he was huge and athletic. An NBA version of JTrain taken to the 10th degree. There's never been anybody like him.
That said, basketball 1) is a team sport and 2) isn't just about offense.
Duncan is a better passer and has a higher basketball IQ (the 2nd leads to him doing lots of little things that make his teammates better and affect the game in other ways). Shaq is also a pain in the ass in the locker room, while Duncan is a great teammate who works with other players and seems to double as a coach.
Regarding point #2, Duncan is a better defender (again, higher basketball IQ means he doesn't fall for fakes, knows when to help out, can goad people into bad shots, etc).
I'd say Duncan is better. I am a Spurs homer, but I think that's still the right call. Shaq is the best in NBA history at dominating the paint, but while that's an important aspect of the game, it's not the only one.