I just came up with a great idea for how the Johto Elite Four could work. (I know that it isn't exactly how it goes in the game, but it should be close enough)
Instead of having a full "Elite Four", you could battle somebody who would stand in as Red at the peak of Mt. Silver. Maybe the Kanto champion could retire and become this person, who would collect the Johto badges? This would definetly require smoothing around the edges, but I like the general idea of it.
