WMG: Mario & Luigi: Superstar Saga

Click here for Wild Mass Guessing for the series as a whole.
The Mine Cart Owner is a ghost.
When you beat the Mysterious Mine Carts, the old guy is seen fading into the image, then remarking "this spot marks the last stop on the long, strange railroad ride of my life". It seems likely that he refers to that spot (the end of the minecart ride) being where he left the mortal coil.
The Mushroom Kingdom's economy is in the crapper.
This explains the ridiculous exchange rates and the rather big inmigrant community in Beanbean Kingdom.
Fawful and Popple are relatives of some kind.
Think about it... Their names rhyme, they both cause mischief and mayhem wherever they go, and they both have something wrong with their head (Fawful is an Talkative Loon, while Popple is a Captain Oblivious to ridiculous extremes). It would make sense. It also helps that Fawful used Popple's boss song for his last fight in Superstar Saga.
Prince Peasley is a Glory Hound who attempted to kill the Mario Bros. during the climax.
The Prince quite obviously enjoys the celebrity status he has with the populace, but throughout the game, he gets rescued or outplayed by the brothers over and over again. By the end of the game, there is transparently no need whatsoever for him to go near Bowletta's castle, but he goes in anyway. Similarly, there was completely no need for him to rig the place with explosives. It achieves absolutely nothing apart from dropping tons of stone debris on his own nation - which fortunately landed in the sea, but since the castle had just been over the major population center, this could be considered dumb luck coming from breathtaking recklessness. It seems far too likely he was hoping to take credit for the "sacrifice" in the aftermath.