You know, make them more meaningful without powercreeping too much.
A simple example would be the old "double-edged sword" mastery (in case you don't remember: with it, you dealt but also took more damage)
A few more examples (just to show the idea, didn't think too hard on the proper numerical balance):
• Pro: you are immune to displacement cc effects (except things like Anivia's wall, where you'd otherwise get stuck inside of something)
• Con: you are also permanently Grounded for the duration of the game
• Pro: your portrait never shows up in the minimap
• Con: you are also always visible through the fog of war on the main window
• Pro: the tower in the lane you are currently in is tougher, does splash damage, fires more often, awards you the gold from the minions it kills, and always focuses enemy champions in range.
• Con: only works on the outer turrets (so it's extremely powerful early but you essentially don't have a keystone in the mid/late game)
• Pro: you do more damage to and get more kill/assist gold from a single enemy champion, that you can mark; you have to mark one before the minions spawn, and if you don't then the closest visible enemy gets auto-marked instead (or the first one who appears if none are visible)
• Con: you get no kill/assist gold from anyone else
**Persistence of vision**
• Pro: you have a "ghost" following you similar to Ekko's ult's, that lasts longer than Ekko's and gives vision of the area (maybe true vision? You'd get to clear wards for free, but you'd also have to backtrack a lot in order to do so)
• Con: you are much easier to follow safely for the enemy
• Pro: whenever you enter a bush, it bursts into flames; enemies who enter that bush are then revealed and take damage; after some time the bush is all burned up, and can't be burned again until it regrows
• Con: bushes on fire or burned up don't hide allies - so there will be no surprise ganks or sitting hidden in bushes for you
**Beauty and the beast**
• Pro: your champion becomes Ahri
• Con: you become Teemo. In real-life.