Generation 3 can be considered the peak of Pokémon, mostly due to when it was released. It was released during the 6th generation of consoles. This generation was a war; Nintendo and others were desperate to create the best games to rival the competition. Pokémon was past its initial peak. Yu-Gi-Oh! was the biggest Pokémon rival at that time.
Generation 3 introduced many new mechanics, like Natures or Abilities.
It featured some of the greatest designed Pokémon, like Flygon, Blaziken, or Salamence.
It also spawned many spin-offs, like Mystery Dungeon.