Expecting Nintendo to use a specific engine for their other franchises is just ... weird ... I don't think they do that with most of their engine specific franchises
What I can see being done is a 2nd 3D Zelda, and mmmmmmmmmmmmmmaybe a 2D Zelda but i'd honestly expect it's own engine for that.
The irony is that a Pokemon game with the BOTW engine would actually make a lot of sense but it won't happen, Gamefreak does things their own way