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Make gyms 'official' battles (like battle tower or competitive battles), don't know how they are called.
> It will teach new players about the pokemon battle system everyone plays
> For each gym you can train new specific pokemon (there's a level limit but you won't level up automatically), so you can have a more varied team in your whole walkthrough instead of sweeping with a powerful one.
> Various expanded regions can be implemented, think of Kanto on Johto when you kick ass with your Johto team
> Gym leaders using actual strategies can be implemented without them being sweeped by raw force
> Removes the awful battle of potions, full restores and revives, also removes the 'buy a lot items and win the league' thing.
I'm currently playing Nameless Fire Red and it feels great, gym leaders and other trainers have their pokemon leveled around your strongest pokemon. It has flaws yes, but if it gets polished it can improve the game significantly.