Perhaps there could be one type of mastery for each of the deck's strengths:
Life Mastery-Win the game with 100 Health (Same as current, would be for the light/life/health gaining decks)
Overkill Master-Win the game with your opponent at -40 or less Health (Would probably have to fix the bug that causes the turn to end early, but it would reward those decks that focus on damage, like fire)
Quantum Mastery-Win the game with a total of 100 Quantum or more (For Rainbow decks, mainly)
Creature Mastery-Win the game with at least 12 Creatures in play (for FFQ/graveyard/mass weenie decks)
Round Table Mastery-Win the game with a Weapon, Shield, Pillar, and Other Permanent in Play (not sure which deck type this would help, but it is an interesting idea I think. Also, when I say Other Permenent, I mean something like Graveyard)
Buffed Mastery-Win the game with a creature in play that has at least 10 more Health than it came into play with (gives something for earth/blessing focused decks)
That's all I have right now. Some of them might be a bit too easy to get, so they might need adjusting, but I think this is the right idea: A type of mastery to cover most types of decks.