Unfortunately, there is no simple solution for a fair system that somehow measures a players "skill". The format of this game simply isn't set up for this level of competition. If made only about the "quality" of games (ie, win loss ratio versus "tough" opponents), then you would just use the appropriate counter/looping team and the only losses you would suffer would be infuriating RNG streaks or equally infuriating random disconnects, battle has already been completed errors, or straight up having your win streak reset errors.
People are frustrated their efforts are not being recognized, so add some additional leaderboards for different things other than grinding points. Make the rewards minimal and crappy, just like the current leaderboard, or just nonexistent. Anyone who really cares just wants to be recognized for effort, the reward for effort ratio for ranked PvP was decidedly in the "not worth" category when PvP 2.0 just launched, let alone now.