>>32539982More open adventure.
Have the player choose any of the eight gyms to go to in any order he/she wants. Depending on how many badges the player has, the gym leader's team would change. That would mean that GameFreak would construct 8 different teams for each of the gym leaders to cover each player's choices.
If you want some difficulty, aside from giving gym leader pokemon unique abilities and different held items, have a lvl cap for each gym leader. Similar to the battle frontier and battle maison which caps at lvl 50, the first gym would cap at lvl 15, the second gym would cap at lvl 25, etc.
Adding to that, give the player different options in tackling the main story. Have them complete the game as a champion, run their own gym, open a lab and become a pokemon professor, a professional breeder, leader of a criminal organization, etc.
This last bit maybe asking for too much, but GF can maybe implement a CoOp mode. You and a friend can team up and double battle npcs, gym leaders and elite four. You can also have the option to stop playing CoOp mid game and go solo if you want to.