My suggestion: After defeating the E4 of Johto, make it possible to now go back to the S.S. Anne. Now at this point, you'd face the previous Gym Leaders, and possibly the E4 if they felt like. The Gym Leaders do confront you before the E4 in Kanto, sort of as a joke. So, I could see this being quite entertaining, as well as giving a reason to revisit Kanto. However, by no means should the fights be simple. They should be high-level endgame PvE. That's just my thoughts. Good idea Tommy.