I had an idea similar to this a while back that I got from reading about the special Black Tyranitar that was considered a Legendary Pokemon in one of the manga. I'd like to see that, some special Pokemon that may look slightly different or different animations than just a simple recoloring of the original. Maybe give them a special unique move that only they can possess and make it impossible to breed for them. (Such as, using Black Tyranitar, say you breed it with a regular Tyranitar, you get a regular Larvitar.)
It would be a lot like the Spiky-Eared Pichu. Make them as rare alternate forms of standard Pokemon.