The "Top" lists benefit Apple, which is why the feature remains. "Top Free" lists apps that have managed to get large user bases, such as Whatsapp and Facebook. These apps help Apple get their customers using more apps, which lock them into iOS. "Top Sales" and "Top Grossing" are even more obvious -- while they do encourage the skeeziest business models, they are apps that are proven to make money, and whatever money they make, Apple gets 30% of that.
"Top" lists won't go away until their presence starts hurting Apple.
"Top" lists won't go away until their presence starts hurting Apple.