I would like to see a game giving Gym leaders (and other important battles) a more "competitive" treatment akin to the official battles these battles are supposed to be.
"Gyms" are basically rooms with a trainer sitting at the end, hiding behind whatever nonsensical puzzle that has nothing to do with Pokémon and waiting for you to challenge them. It doesn't make sense.
I think they should be more like mini-tournaments or arenas where you compete against a few other trainers, and the winner gets the right to challenge the gym leader. And while inside a Gym, Battle style locked to Set and no use of cheese items like Full Restores, potions, or X items (held items only, as in competitive) to make it feel more like official battles with no unfair advantages hand-holding the player. The Radical Red rom hack already does some of this.