Maybe this would fix masteries
Bring back the old masteries and create a separate page like a "keystone page" that you can select only a certain amount of abilities that synergizes with your champ. Because I would love thunderlords or stormraiders surge on certain champs but I like the armor pen or magic pen from the ferocity tree alot more better. Masteries would be better as a stat change and Keystones would be more of a style on what you play.
Ex: Currently there are 3 choices for each section you can choose up to one from each they could add more keystones for a more variety to choose from.
Edit 1: For example many mid lane champs would like thunderlords over deathfire but dont want to sacrifice armor or magic pen for it and tbh thunderlords doesnt belong in the cunning tree at all