It kinda feels weird now when starting in Johto and going to Kanto because Kanto didn't feel as fleshed out and only there to pad the game. On the other hand, I would be happy if they announced Johto as reasonably priced DLC. Remove the water segment separating New Bark Town and Victory Road and allow players to play both regions in any way they want. People may not like it but I think level/difficulty scaling would make it feel more fluid. After initiating a battle with a gym leader or during an important story segment, the NPCs' pokemon in the area/story are "locked in" and the difficulty for remaining uncompleted areas would increase by one. This way somebody could complete Johto first and with all the HMs, complete the gyms in Kanto in any order while still facing increasing difficulty. If somebody wanted to, they could get all the badges from both regions and do both rounds of Elite Four back to back. Which set of Elite Four you face first would be dependant on which set of badges you complete first and being able to fight anyone of them at any time after defeating "Red" would be cool.