I can try guessing the name of the villains, if they happen to be a duo:
Cynthia and Caesar (Synthesizer)
Would fit antagonists that are capable of magic and otherwise unnatural stuff, and synthesizers contrast against the friendly, folksy sound of ukeleles.
On what they would look like, Caesar could be a lanky crocodile with butterfly wings, so we could have some humor at his expense, while providing him the means to be worthy platforming rival to the heroes. Cynthia, on the other hand, could be a mask that creates a body for itself, to get that shaman/Majora vibe.
In that case, I think that having a Villainous Couple dynamic would provide a fresh take on the usual villains in Rare's past works. Caesar could act as an obvious bad guy, while Cynthia would lead the player into trusting her as an ally. Then, at the final confrontation, Cynthia would turn on Yooka and Laylee, and you would fight a villainous duo as the final boss.