I was aware of Rare, Skip, and Fuse's presence in WarioWare, but I opted to use the words "series" as I felt it was more feasible that those games were added for being parts of EAD-created franchises (Mii, Mario, and Donkey Kong), though now you bring up rights ownership that does make a roughly equal amount of sense. I dunno how Nintendo handles content with shared copyrights when a company goes bankrupt so I won't edit. (I do know that Nintendo tend not to acknowledge Western-only games, even when made by defunct studios like Tin Star was, with StarTropics as an exception, but I could imagine a billion reasons for both that and why StarTropics in particular gets special treatment)

I'd love to see Mole Mania get a microgame some time, that was an anonymous work of Softnica IIRC. Perhaps one of the modern games from G&W Gallery, which was by TOSE. Drill Dozer is my favourite Ninty franchise total, and one that would work well for a WarioWare microgame, but - maybe this is just all the issues Pokemon has had in crossovers speaking - Game Freak strikes me as a way higher hurdle even without Pikachu involved.

There is a third category of studio represented in WarioWare games: defunct ones/ones that had the rights for their games seemingly revert to Nintendo. Move It! has a Mario Pinball Land microgame, which was developed by the now-defunct Fuse Games, as well as a Wii Play Motion microgame based on Pose Mii Plus, a subgame developed by Skip Ltd. The Donkey Kong Country microgame in Gold would count for the latter, as Rare is still around, but doesn't really actively work with Nintendo anymore because they're owned by Microsoft.

As an aside, I do wonder if we'll see more microgames derived from Nintendo subsidiaries in the future. Retro Studios is the only one to get any so far, I believe, but there's definitely room for NST, Monolith Soft, Next Level Games, and maybe Brownie Brown's old games to get microgames.