Hakeem's peak was higher. There are few fans on the board who are going to debate that.
However, Tim has put together a sustained period of dominance that few NBA players are ever going to match. He is a much better passer than Hakeem, and plays much smarter defense, which refutes your statement that athleticism is able to trump this category. If defense = athleticism, the Spurs would not have more than a single banner in the rafters, if that.
And he's not done yet. Really, if Timmy ends up with 15 ASGs or more in his career and 5+ rings, how are you going to possibly argue that Hakeem was a better player over the course of an entire career? Tim Duncan's game is one that, in spite of posting excellent statistics across the board, defies those statistics in the same motion. He is a perfect example of what stats DO NOT tell you about the game of basketball.
So you can take Hakeem's incredible number of post moves and offensive abilities, you can take his dream hook, and his vaunted athleticism. I'll take Duncan's consistently heady play, his BB IQ that is almost unparalleled across all of the major sports, his ability to control the game when he doesn't have the ball, his passing skills, his incredible clutch play, and the four banners hanging from the rafters that all resulted from him being the best power forward the league has ever seen. The part that puts it over the edge for me is that Tim isn't even CLOSE to being done yet, and may have 6 or 7 rings when everything is said and finished, at which point the comparisons to Hakeem would cease and talk about whether Duncan should be in the top 5 of all time would start.