Opening up every treasure chest in the game unlocks the Jon and Leno action figure after you beat the game.
Colonel Cappriccola is actually Jon in disguise who secretly helps Musashi throughout the game as he wants revenge against Fuhrer Flatski for the death of his parents. He is the prince of the Thirstquencher empire.
The boss fight with Topo is the only one in the game that's actually a minigame.
The biggest mystery of this game happens during the ending with the King and Queen as you never see what happens after Musashi reveals himself to them. The after credits scene provides a bit of closure as Musashi returns the Sword Of Luminescence back to where he found it at the beginning of the game.
Every musician you free from a Binchotite changes the theme at Allucaneet Palace after you speak with them.