Notes on a BOTW/TOTK Atlantis: The Lost Empire au
Milo Thatch - Zelda -> it just makes more sense for her personality to make her the passionate scholar rather than the warrior princess.
Kida Nedakh - Link -> less an actual prince and more of an out-of-time wild child who was taken in by the king and queen.
Preston Whitmore - Impa
Commander Lyle Rourke - Ganondorf
Lieutenant Helga Sinclair - Riju -> much less overtly villainous than Helga, and in fact turns against Ganondorf pretty quickly once he lays a hand on the royal family. She's also not the one who recruits Zelda; Paya is the one who takes Helga's role in that particular instance.
Dr. Joshua Sweet - Sidon -> the Zora have healing powers and he is one gigantic sweetheart.
Audrey Rocio Ramirez - Tulin -> young airship mechanic. Teba was part of the expedition that found the Journal/Tablet.
Vincenzo "Vinny" Santorini - Yunobo -> because of the whole explosions thing, though the personality is drastically different.
Gaëtan "Mole" Molière - Josha -> up the child prodigy aspect rather than Mole's overwhelming weirdness (given that Josha is the head of the Depths investigation team this just makes sense to me).
Wilhemina Packard - Purah
Jebidiah "Cookie" Farnsworth - Robbie -> these two are undercover as the communications officer and cook respectively and were in fact tasked by Impa to keep an eye on Ganondorf (all those moments where Packard is gossiping with her friend Marge instead of watching comms? That's Purah reporting directly to Impa through code); they take over the expedition after Ganondorf betrays everyone.
Kakeshim Nedakh - Rauru -> create a role for Mineru - makes more sense for her to become queen after Rauru's death than for Link to become king.
The Queen - Sonia
The Leviathan is either the Colgera or a giant Flux Construct. Maybe even a literal Divine Beast.
I am open to better ideas.