So I put together a list of the remaining ones from the popular games and the unused ones. Not many stand out to me.

Oot

• Nabooru
• Saria
• Kaelora Gaebora
• Rauru
• Dampe
• Kotake/Koume - twinrova

Majora’s Mask

• Happy Mask Salesman
• Mikau
• Darmani III
• Deku Butler’s Son
• Postman
• Giants

Wind Waker

• Beedle
• Cyclos
• Zephos
• Orca

Twilight Princess

• Darbus
• Rutela
• Ralis
• Yeta/Yeto

Skyward Sword

• loftwing
• Demise
• Groose
• Scrapper
• Batreaux
• Guld

ALBW

• Hilda
• Sahasrahla
• Gulley
• Seres
• Osfala
• Irene
• Oren
• Rosso
• Mother Maiamai

AttP

• Agahnim
• Sahasrahla
• Flute Boy
• Dwarven Swordsmiths

These I don’t remember as much

Minish Cap

• Ezlo
• Vaati

Oracles

• din
• nayru
• farore
• Maple
• General Onox
• Moosh
• Kotake/Koume - Twinrova
• Ricky
• Great Moblin
• Queen Ambi

Phantom Hourglass

• Bellum
• Linebeck
• King Mutoh
• Zauz

Spirit Tracks

• Byrne
• Demon Cole
• Malladus
• Phantom Zelda

Could be a cool idea to have a game where you cycle through versions of reincarnations. Maybe Twinrova shenanigans

• Link
• Zelda
• Impa
• Ganandorf
• Beedle,
• Postman
• Tingle
• Epona
• Dampe
• King of Hyrule
• Great Fairy
• Kotake/Koume
• Kaelora Gaebora

but I think you’d be limited.