Gym battles like Whitney in Goldenrod City that actually require tactics then spaming buttons.
Create gyms that have certain environmental effects such as Rainy Day or Sun or perhaps hailstorm/sandstorm and of course the gym leader pokemon dont get hurt.
Give some of the Champions Legendary Pokemon. Like why cant Red have a Lvl 80 Mewto on Mount Silver lol?
Create mini bosses such as a very high level trainer then usually who appears that you pass to defeat instead of "random power outages'