Gen 2 and Gen 3 from a competative metagame standpoint.
Gen 2 added:
Breeding (also Genders and Baby pokemon)
Steel and Dark types
Equipable Items
Poke'rus
Shiny Pokemon
IV's inheritance
Gen 3 added:
Abilities
Natures
Weather Conditions
Double Battles
International Trading
EV, IV, and Shiny Pokemon system overhaul (nearly same system today)
Upgrade to 60 FPS (been that way ever since)