what would be cool is if the last gym leader was your rival from Gold Silver and Crystal. That would be cool since he is pretty strong, but they would have to give him a certain type. Perhaps Dark or Normal? Or maby we should just stick with electric, I don't really care. Also, Palmer should be the Champion, Volkner should run the battle tower, and Cynthia should be like Steven from Emerald, and go into hiding or something. You could still fight her like you could Steven, but she would be in some weird added on area like Steven was. However, she should still be part of the story line, like giving you psyduck potion and other things.
Couldn't think of anything better to put here, so... yeah...