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Make a clear distinction between minor and major legendaries; rebalance them so major legends > minor legends > ordinary Pokemon is the norm. Then give players an option to specify before battles how many and what type of legendaries are allowed per team (1 major, 3-1 minor or none at all).
Or just don't do anything at all because legendary mons are still just mons like all others. Competitive Pokemon has a lot worse problems than that.
