I don't put too much stock in the 'Duck Hunt = Banjo' theory, because I think it's just a big coincidence that Swordfighter and Duck Hunt crash the game in Century Smash (has this even been proven yet?). However, I've seen a baffling amount of people argue that Duck Hunt can impossibly serve as a base for Banjo, because Banjo is a biped, while Duck Hunt is a quadruped. I think these people are missing the point. We are only discussing bases, not animations. This is Duck Hunt's base model from Smash 4:
Duck Hunt standing on four legs is an animation. If Banjo were to inherit from Duck Hunt, he would obviously have different animations and stand on two legs.
Furthermore, Duck Hunt consists of two separate models. I believe Banjo and Kazooie were two separate models as well, but I'm not 100% sure. Would be nice if someone could confirm that. All I was able to find was this model from Banjo-Tooie's multiplayer.
All in all, Duck Hunt is a suitable base for Banjo and I don't understand why some people are so adamant about denying this. Once again, I doubt the theory means anything, but that's not because of Banjo being a biped.