I don't know if I would like a fantasy author to write the entire script, but I'd definitely say they should get involved in a sort of overseer role.

I don't think an author would be able to implement the linkages between story, history, culture with the gameplay, which is necessary for a game. Looking at VII, materia was critical to both gameplay and story. GFs in VIII and Espers in XII were less involved from a story side (apart from making people forget), but Eidolons in IX, Espers in VI, Aeons in X and the whole l'Cie thing in XIII were critical to the story.

However, I think an author would make dialogue more believable, get rid of some ridiculous melodramas and twists and make sure there aren't any really silly things (GF memory loss and laughing scenes for example) don't occur, or are at least toned down.