If you inspect the steering wheel of The Princess Peach cruise ship while Bobby the Bo-omb is next to Mario, he will remark how he once dreamed of being a captain or an admiral. This is a reference to Admiral Bobbery, Mario's Bo-omb partner from Paper Mario: The Thousand-Year Door

The Sombrero Guy from Autumn Mountain may have been planned to be a temporary party member just like Spike and Bone Goomba, but was left out. Altering the code through save file hacking makes the character fully functional and adds an otherwise unused graphic to the pause menu.