The way that I interpret the WarioWare + Rhythm Heaven universe (in my headcanon anyway) is that Mario games are metafictional, but Mario is real, and Mario and Wario are essentially actors who do some kind of acting for Nintendo games. The other WarioWare characters are basically absolute nobodies, hence why they never show up in Mario games.
I am also forced to assume that Wario and Waluigi do not like each other in “real life” and are forced to tolerate each other for their acting gigs, hence why Waluigi never appears in WarioWare (although, on the other hand, Mario and Wario’s rivalry is real, or at least it is from Wario’s perspective.)