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I had this idea for a fangame called Pokemon Topaz (Also, Pokemon Jasper as the secondary version). The cover legends are Raikou for Topaz and Entei for Jasper. It's essentially the B2/W2 of G/S/C, taking place 10 years or so after the original. The evil organisation (no name yet rip) want to capture the cover legendary beast and unlock it's true power (Probably mega evolution, but something else could be a possibility). Also, certain Pokemon have Johtoan forms. (I don't know how these'd play out, however)
Say how autistic this idea is if you wish.