Well...hmm...this one's actually tough.
In the case of Amaterasu and Banjo, I think I'm going to go Banjo. It's nothing against Amaterasu, who I would also like to see, but Banjo is more ingrained in Nintendo's history, despite the Rare drama. Probably moreso, however, is that I can see him as a character more than I can Amaterasu; he seems like he'd have more at his disposal.
As for Skull Kid vs. Isaac, I'm going Isaac for partially the same reasons. He seems like he'd be an interesting character should he be implemented, and as much as I'd love to see SK's final smash in this, I'd have to say that Isaac has more potential.