If I Annexed Nintendo
Super Wario Bros.
A total moral/aesthetic inversion of the Mario universe. The inverted version of Bowser rules the land with an iron grip of fuzzy pastel kindness. You play as Wario and Waluigi, concocting absurd Rube Goldberg supervillain schemes to ruin it. The inverted versions of Peach and Daisy are your rivals, who keep crossing paths with you and sabotaging your schemes with their own.
It's as cheery and fun as any other Mario game, but with some really neat subtext about how evil is innately self-defeating but can wreck a lot along the way. And in interludes with Bowser, there's some great reflections on how stringent pacifism must reckon with people who cannot be peacefully swayed.
A Decent Paper Mario
Super Mario Odyssey was a burst of gloriously weird, clever game design. I'd love to see that spirit of innovation merged with the magnificently strange writing from Paper Mario: TTYD.
Keep the straightforwardly cartoony style, but with subtle material textures: felt, cardboard, tissue paper, etc.
Shoji doors as a mechanic?
Combat could be on a grid, like a condensed Fire Emblem.
Possible partners: a mineral Chain Chomp, a deep-sea Blooper, a grizzled veteran Bullet Bill, and a reformed former X-Naut troop.
Infighting In Bowser's Army
The immense, diverse coalition of Bowser's military is brittle at best. Whenever he leaves for tennis or go-karting, factions within it vie for power and control without outright staging a coup.
You are an entry-level recruit in a faction of your choice: the Chain Chomp keepers, the necromancers who maintain the Boos and Dry Bones, the Bob-omb Corps, a cabal of X-Naut spies, or more. Gameplay is like Fire Emblem without combat, trying to carefully balance the demands and interests of your partners and rivals to ascend the ranks.
Do Literally Anything With F-Zero
Making a difficult, high-speed racing game seems out of Nintendo's wheelhouse, and might step on the toes of Mario Kart anyway. Maybe make a whole open-world RPG in the F-Zero world, with some incidental racing as a plot element?