• Super Mario RPG: Legend of the Seven Stars
• Super Paper Mario
• Mario & Luigi: Superstar Saga
• Paper Mario: the Origami King

Depending on your definition of ‘sidekick’, these may also count:

• every Mario Party game
• every Mario Kart game
• every Mario & Sonic Olympics game
• Super Smash Bros Melee, Brawl and Ultimate
• Mario & Luigi: Bowser’s Inside Story

There might be more I’m forgetting.

Bowsette may not be Nintendo canon, but it sure as hell is fan canon.

Well, I’m pretty sure there were instances where Mario and Bowser cooperated. But it doesn’t matter, because even if only 2 answers make sense, the joke already works.