You Should Be Able to Choose Whether Thunderlord's Decree Deals Physical or Magical Damage
I think this would fix the dilemma of balancing it on AD Champions, mainly assassins. Before the buff it has received last patch which buffed its bonus AD ratio to be 30% instead of 20%, it was a bit lackluster on AD casters compared to AP ones, now the opposite of that is the case. Do you remember the icon of your keystone mastery that shows up when you press tab? If you rightclick it, it should change it's damage from magical to physical damage and the other way around, so it is able to synergize better with penetration granted from the Precision mastery, flatpen runes and the pen granted from Youmuu's, maybe even the bonus armor pen that the Last Whisper upgrades give you though I think they are not really that good on most Assassin's. Right now the juicy Pen you get from all of this is wasted on most AD casters while all AP casters can make full use of the magic penetration they have. This way the buff to its ratio could also be reverted because it wouldn't be needed anymore.
On the same note this could be done with other masteries aswell. Fervor of Battle for example would be really good on Teemo and Kayle if it would be able to deal magical instead of physical damage. There are also AD Casters who can constantly deal ability damage to reproc Deathfire Grasp and have a lot of penetration in their builds and kits like for example Urgot and Garen but can't make use of it because Deathfire Grasp deals magical damage.