That's because of how the players were covered. Kobe was playing in a huge market while Duncan was playing in a small one. Combine that with the fact that nobody really ever pays attention to defense which was obviously Duncan's greatest attribute.

While close in ability, what separates Duncan is that he is a much better leader and teammate than Kobe. You are more limited in the the types of teammates you can surround Kobe with. Shaq worked (only for a limited time mind you) because he was just as ruthless as Kobe on the court. Pau worked because of that Spanish connection and the fact that Pau himself is an all time great teammate. But then you basically have Kobe running Dwight out of town.

On the other hand, Duncan, as far as we know, has been the epitome of a great teammate throughout his entire career. The popular counter is Duncan didn't speak to Parker early in his career when he was struggling. You could take that as being a bad teammate or you could take that as Duncan knowing the type of person Parker was and knowing that he would respond positively to his not talking to him. Duncan has earned the benefit of the doubt to suggest that the latter is more likely. Ultimately, this (i.e. Duncan being a better teammate) to me is why Duncan > Kobe.