Double battles, abilities, natures — the competitive reboot.
Ruby, Sapphire, Emerald (and the Omega Ruby / Alpha Sapphire remakes) · Released 2002
Hoenn is the Gen 3 region, and the single biggest mechanics shake-up in Pokémon history. Ruby & Sapphire added abilities (Pokémon-specific passive effects), natures (stat-modifying personality traits), EVs (effort values — replacing Gen 1/2 stat experience), double battles, and weather teams. Almost every concept that shapes modern competitive Pokémon — Drought Ninetales, Sand Stream Tyranitar, Swift Swim rain — was invented in Hoenn.
Hoenn is based on Kyushu, Japan's southwest island. Its tropical climate, heavy rain and volcanic geography directly inspired the game's theme of weather and climate catastrophe (Kyogre causing endless rain, Groudon causing endless sun). The elevated land / sea / sky trio of Groudon / Kyogre / Rayquaza mirrors Japanese Shinto cosmology.
Ruby & Sapphire were the first Pokémon games to run on the Game Boy Advance's 32-bit hardware, which is why Gen 3 broke save compatibility with Gens 1 and 2 — the old games couldn't read the new Pokémon data structure, and there was no way to transfer mons forward until Pal Park in Gen 4.
Ruby and Sapphire introduced abilities and natures, and between them they turned Pokémon from a game about species into a game about individual specimens. Two Charizards with different natures and abilities are genuinely different Pokémon, which is the foundation of every competitive format since.
Effort values were formalised here too, replacing Gen 1 and 2's opaque stat experience with a system players could deliberately train against. Double battles debuted in Hoenn and eventually became the standard format for official Video Game Championship play.
Weather was the other lasting contribution. Drought, Drizzle and Sand Stream gave the game its first genuinely strategic field control, and weather teams remain a defining archetype twenty years later.
Hoenn produced an unusual number of enduring competitive Pokémon: Salamence, Metagross, Blaziken, Swampert, Gardevoir and Milotic have all spent time in the highest tiers, and several received Mega forms in Generation 6 that pushed them higher still.
Kyogre and Groudon are worth singling out. Their Primal forms in Omega Ruby and Alpha Sapphire produced permanent, unremovable weather — a strength level that effectively required their own restricted format.
Abilities, natures, formalised effort values, double battles, weather-setting abilities and the Pokémon Contest system. Abilities and natures in particular transformed competitive play by making individual Pokémon meaningfully different from one another.
135 new Pokémon, numbered #252 Treecko through #386 Deoxys. Ruby and Sapphire were also the first games unable to trade with earlier generations, which made Hoenn feel like a fresh start for the series.
Salamence, Metagross and Blaziken have all been top-tier across multiple generations, and Blaziken's Speed Boost ability was strong enough to see it banned from several formats. Among legendaries, Primal Kyogre and Primal Groudon sit in a restricted tier of their own.