Super Mario RPG/WMG

This is the Final mario adventure chronologically
Either Bowser would stop kidnapping Peach out of gratitude for her help in retaking his castle, or more likely, would be smart enough to realize that both Mario AND Peach are strong enough to take out villains much more powerful than him.
 * Bowser is Princess Kidnapping junky. Regardless of whatever gratitude he might have, he still relapses.

In this game, Mario is a Jumplomancer
He is capable of some truly epic leaps (it's possible, for example, to get 100 jumps in a row) that only do falling damage on the opponent and not himself; in the case of 100 jumps, this earns him a nifty item; in another, he convinces a terrified citizen of Mushroom Kingdom that he is indeed the legendary Mario by jumping.

That second Mario in Jonathan Jones's ship is actually a Duplighost.
He must've been spying on Mario from off-screen then decided to turn into him for kicks. He snuck off to that room off to the side, but Mario ended up walking in on him.

The "higher authority" that Geno answers to is the Star Spirits from Paper Mario.
When not in doll form, Geno appears as a small sparkling star. He's a grown "star" like the Star Spirits, and they're his superiors.