It may be a nintendo classic, but I guess they couldn’t think of anything good

Unlike other series featured in it Nintendo only has partial ownership over Pokemon, so maybe they didn't think it was worth the effort securing the rights to use it there, or maybe they just couldn't.

That’s… exactly what I wanted to say originally.

Yeah, Nintendo can't just put Pokémon in their other games. They need permission from The Pokémon Company. It's also why Pokémon hasn't made appearances in games like Mario Kart or Kirby's Great Cave Offensive.

As I remember in the original Warioware for GBA if you will do nothing at the nailing boss the guy will call you a Slowpoke, which might be the only reference. For some reason this line was changed in the remake.

That didn't stop them from putting Pokémon in Super Smash Brothers.

I could've sworn a Pokeball was one of the treasures in the Great Cave Offensive, but I guess I was wrong.

Pit said the word Tentafool in Kid Icarus: Uprising, but I'm not sure if that counts.

Yes, but Super Smash Bros is a crossover franchise with Pokemon as playable characters, maybe they didn't think it was worth securing the licence for a small cameo in a Wario game.