This is actually an excellent idea. Have a rule where only one character (or maybe 1 PC or 1 NPC) per campaign may have the feat at any given time.
I've actually toyed with doing a prestige class/feat supplement that featured this concept. For example, Arthur and Aragorn belong to the True King PrC, which can only belong to one character.
Another variant is to take a class or ability that already exists and limit it. What of there was only ever one paladin in the world? What about one cleric in a world where the gods never show themselves?