Cunning is too universal and shares too much with Resolve. This is why Thunderlord's is used most.

The current mastery system is in a crisis. The most obvious symptom is the reign of Thunderlord's decree, but I think the problem is a much deeper then one over powered keystone.

The issue is the universality of the cunning tree and thunderlord's decree. In this tree you get sustain, utility, and damage. Arguably as much damage as you get in Ferocity. 18 point in Cunning in universally useful, while some of the other keystones have some niche users (Grasp of the Undying is silly good top) the fact remains that every champ in the game is comfortable with thunderlords and 18 cunning. You still have 12 points to hit the high notes of the other trees, so if you're a tank you still can double down on sustain and beef with 12 points in Cunning, and if you're anyone else you can get more damage and sustain in Ferocity.

Right now the best thing Riot could do is take a good look at the offensive options that are split between Ferocity and Cunning. Resolve is in a good place right now with a clear strength and cost. But the identity of the other trees is mixed to the point that one is clearly better then the other for the majority of users. To be honest I'd take the sustain masteries out of ferocity and the damage masteries out of cunning and swap the two. They'd have to be renamed but it would at least resolve their game-play identities.