Pruning abilities you never click isn't pruning anything.
It removes button bloat, but it doesn't prune things. Consolidating duplicate abilities is better (Instead of having an ability that generates 1 resource and a short-cooldown ability that generates 4 resource, remove the 4 resource and buff the other to 2 resource generation, for example)
I hope how you can see that removing abilities that you never use anyways isn't going to net real changes, except button bloat. While they should get rid of them, there is still a lot of actual pruning to do in this game.