For the most part, I'm not a big fan of either mastery system we've had for this reason. I don't like the arbitrary stat crutch that masteries represent. Not quite as much as I hate the arbitrary crutch that runes are. I think there are some better balancing reasons for masteries existing, but I'd rather see the majority of masteries which translate into straightforward power for a champion removed and have that power reabsorbed into individual champions.
I don't mind masteries being somewhat more impactful, but only in certain areas. Now, maybe I'm misguided in these thoughts, but I feel like the best purpose of the mastery system in League as it is now should be to allow the following to occur:
-Poorly-scaling early game customization which allows lane flexibility
Allowing champions to tweak their experience slightly to accommodate what kind of lane and opponents they are going to be up against, with some options to gamble for slight advantages based on how they think they will perform. Accomplished by very minimal stat allotment, situational sustain option tradeoffs and such.
-Granting some support to roles which must function with less reliable income streams.
By which I mean supports and junglers, of course. Things like bandit, out-of-combat movement and sustain options, and large monster specific effects are kinds of things which work more specifically to aid these kinds of champions throughout the game without being overbearing on others.
-Less kit synergistic gameplay options.
Objective control/vision options like the scouting mastery we used to have, situational movement, ally dependent buffs like the new assassain mastery, performance dependent masteries like Dangerous Game or Bounty Hunter. All of these kinds of option I feel have a healthier space to work with and be meaningful decisions according to individual gameplay preferences if they aren't competing with straight up reliable damage and defense options.
In particular, I don't think pseudo-ability level damage and defenses are ever going to be in a satisfying place. They are always going to mess with the intended combat interactions of a champion's kit and favor some champions over others in a non-meaningful way. You can balance the outliers around these masteries, but why create another complication in the process?