I thought about it this way. If I had to choose between any
ANY
Pokémon rep (especially one from Gen VII or later)
or Banjo-Kazooie being in the game, I couldn't imagine choosing the Pokémon rep. That's all that playable Pokémon in Smash feel like. They're just promotions for the most recent games instead of something that everyone wants. The hoops you'd have to go through to get Banjo-Kazooie compared to some "obligatory entry" like Incineroar or Decidueye makes one feel like something for the fans and the others like filler.