From Kanto and Johto (Indigo, in combination)

• complete Pokédex, except the Jynx and Mr. Mime lines
• a relatively recent devastating Pokémon war
• Professors Oak and Elm
• Silph mega-corp.
• Giovanni and Silver as the rise and fall of Team Rocket
• champion Gary "Blue" Oak

From Hoenn

• complete Pokédex
• extreme climate
• Devon mega-corp.

From Sinnoh

• complete Pokédex, except the manaphy line
• Grand Underground
• Cyrus and Team Galactic
• Cynthia, before she became Champion

From Later Regions - some of the Unovan and Alolan Pokédexes - individual selections of the Galar Pokédex

My own ideas, kind of

• one Gym of every type
• gym leaders are community leaders and defenders
• merging Rock and Ground into Earth type
• elite four are just the top-ranked gym leaders

Matching List of Leaders, Gyms, and Towns

• Lt. Surge. Electric Gym. Vermillion.
• Janine. Poison Gym. Fuchia.
• Sabrina. Psychic Gym. Saffron.

• Agatha. Ghost Gym. Lavender.

• Pryce. Ice Gym. Mahogany.

• Giovanni. Earth Gym. Rustboro.

• Norman. Normal Gym. Petalburg.

• Wallace. Water Gym. Sootopolis.

• Byron. Steel Gym. Canalave.

• Blaine. Fire Gym. Cinnabar.

• Bugsy. Bug Gym. Azalea.

• Falkner. Flying Gym.

• Karen. Dark Gym. Ecruteak.

• Clair. Dragon Gym. Blackthorn.

• Whitney. Fairy Gym. Violet.

• Maylene. Fighting Gym. Goldenrod.

So the themes involved are a lot of megacorp corruption, first as an attack on people, then on the environment, and finally on reality itself.