I don't think that it's going to happen but I'll give it a shot. I know Pokémon the best.
Kanto
Leader: Red
Capital: Pallet Town
Agenda: Gotta Catch Em All!: Likes to have the most animal resources. Dislikes Civs with more animal resources than him.
LA: Pokémon Power- Gain gold whenever you improve a new animal resource. Gain combat strength for every animal resource you have. Gains the Pikachu UU at the beginning of the game.
UA: Kanto Region- Each city you build has specific abilities and will be named accordingly, sometimes, to the features around the city.
UU: Pikachu? faster Scout replacement?
UU: Mewtwo: Special air unit with high combat strength and can only have one at a time.
UB: Pokémon Research Lab- Replaces Research Lab- Extra Science for every adjacent pasture. Needed to produce Mewtwo UU.
City List:
Viridian City- Forests tiles provide science.
Pewter City- Artifact Museums and Natural History Museum can hold more artifacts.
Cerulean City- Units trained here receive faster movement on roads.
Vermillion City- Enhanced naval production if built on coast. Harbor does not need a lighthouse for extra trader capacity.
Celadon City- Markets provide more gold as do Shopping Malls.
Saffron City- 5% faster population growth for every district in this city.
Lavender Town- Gain culture for every unit killed from this city.
Fuchsia City- National Park in this city will have higher appeal and amenities.
Seafoam Islands-Culture for every reef and more tourism for seaside resorts.
Cinnabar Island- Science buildings in this city gain more science adjacent to a natural wonder.
Indigo Plateau- Entertainment Complexes gain extra amenities from Arenas and Stadiums
What would Red's favoured victory condition be?
Here are some to start with:
Mario:
Civ: Mushroom Kingdom
Leader: Peach
Capital: Toad Town
Unique Unit: Plumber (replaces Military Engineer; can attack and construct Pipes and other Military Engineer improvements)
Unique Improvement: Pipes (provides instantaneous travel between pipes; one set of pipes can be built per city; provides gold and can be built before researching Flight)
Favoured Victory Condition: Science (highest priority) or Culture (fallback)
Zelda:
Civ: Hyrule
Leader: Zelda
Capital: Hyrule Castle Town
Other cities: Kakariko
Leader Unique Ability: Chosen by the Wise Golden Goddess Nayru (Sacred Groves generate science and Campuses generate faith)
Unique Unit: Hylian Knight (can only be purchased with faith, use the Warrior Monk promotion tree, and are stronger during Dark Ages)
Unique District: Sacred Grove (replaces the Holy Site, boosts loyalty, and can recruit Hylian Knights (requires Temple of Time, which replaces the Temple))
Favoured Victory Condition: Religious (highest priority) or Science/Culture (fallback)
Kirby:
Civ: Dream Land
Leader: Dedede
Capital: Mount Dedede/Cappy Town
Agenda: Gluttonous (likes civs that don't produce as much food as Dream Land, dislikes civs that produce more food)
Leader Unique Ability: He's King and That's That (food surpluses boost loyalty)
Civ Unique Ability: Dreaming a Better Tomorrow (food is used as currency to purchase units and to provide unit and governor upkeep; food can be used as an alternative to gold or faith to recruit a Great Person, food yields are doubled; gold yields are reduced 25%)
Civ Unique Unit: Kirby (can only be purchased with food; can absorb other civs' unique units' attributes)
Leader Unique Unit: Waddle Dee (can only be purchased with food)
Unique Building: Fountain of Dreams (replaces the Monument, provides culture, food, and amenities)
Favoured Victory Condition: Domination (highest priority) or Science (fallback)
You can come up with any suggestions on how to improve these civs or add new civs.