Wario Land always had minigames that play different from the main game, except maybe Shake It. I can't remember if Shake It had any. My idea is to have Mona be playable for these sections, She would unlock coins/treasure/lives/keys that would help Wario on his adventure.
Another idea is to...
I like the point you made about Shokora having her own minigames, so she would be a good fit for Wario's microgame company. I want to see Shokora return, because she and Wario had a good camaraderie.
Time for another playthrough. I'm also hoping that Nintendo will take note of how many people are playing this on NSO to test the waters of potentially reviving the series.