I think there are different ways of looking at it. There is definitely an argument for Shaq over Duncan.
But look at it this way. The article/list is talking about best number 1 draft picks over the last 23 years. If you talk about franchises making the right pick or best pick, consider what each pick did for the respective franchise that drafted them. Shaq has had a legendary career in his own right. Despite all his success, what did he give to the team that drafted him, the Orlando Magic? One NBA Finals appearance and then destroyed it by leaving without even getting the compensation for leaving. What did Tim Duncan bring to the team that drafted him, the Spurs? Four les, two league MVPs, and sustained success over 10 years.
Shaq's success matches Duncan's on essentially all levels. He also destroyed three franchises along the way.
His lack of loyalty and his selfish ego made him an all time great player that didn't allow for the team that drafted him to reap the rewards of his greatness.
I think Tim Duncan is the correct choice for the #1 overall spot in this list.