Taking a percentage of sales is a very astute observation. It's equivalent in economics to what we call sharecropping, another process in which you take a percentage. The percentage is done to give the right incentive to the mall owner to put in the right mix of stores. As a retailer, you don't want another restaurant right beside you. You don't want another store competing.
By giving the owner part of the rent in a share, they want to maximize the total revenue of the mall. Allowing them to take that percentage gives them the right incentive. It's almost like an interchange fee; it provides the correct incentives to the various parties.