There are two things that I'm really hoping for, but I'm almost certain they won't be included in the games. First, I want GF to re-think what it means to be Pokémon League Champion. When the player beats the E4/Champ, they become Champion. Yet, the next time you face the E4, its as if it never happened. When you become Champ, and as you complete the post-game, NPCs should react to the fact that you're Champion. Also, you should receive challenges from budding trainers who have beat the E4 and are hungry for your title. Maybe your rival could end up challenging you, or the former champion? Also, becoming Champ should unlock a feature called "Champion battle", where you battle your friends who are also Champs over wireless communication. If you win, your trainer data should be written into your friend's game so that you become Champion in their universe. Your friend will then have to challenge the E4 and beat you to regain their title. That way, you could spread your Championship reign beyond simply your game!
Also, as a small detail, I want the Kalos region to include some kind of Pokemon government institution. These would be the people who certify the gym leaders and E4, decide which cities will have gyms, regulate what's sold in poke-marts across the region, monitor the Pokémon population across Kalos, etc