Thunderlords shouldn't deal just magic damage.
TL:DR Change it so that Thunderlords's damage type changes between physical and magic depending on what the player is stacking. If they have more AP? Magic Damage. If they have more AD? Physical damage.
So I woke up, got outta bed, looked in a mirror and said to myself "Why is graves calling down a bolt of lightning?"
It occurred to me that a lot of why thunderlords FEELS like the best choice is because all the AD champs get a way to get around armor. Stack all the AD you want and suddenly you have a blast of magic damage at your 3rd attack that might as well be an execution skill.
And if that doesn't work, just throw the damn mastery out the window, I give up.