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 immigrant community in the 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.
Prince Peasley has a crush on Luigi.Think about it. He gives Luigi a rose as a sign allowing admittance into the castle saying that "it suits your green", he finds Luigi's 'Luigi Dunk' amusing and appears to take the challenge in finding the Beanstar pieces very seriously when he strikes Luigi in the rear with his rapier who then gives a Luminescent Blush. Did he really have to do that? He's basically leading Luigi on at this point.
The Belly Blech Worm is still at large.When you cure Queen Bean of the Belly Blech Worm with the Chuckola Reserve, she burps out the worm. but unlike other bosses with supernatural origins, they tend to outright explode into nothingness. what im saying is that the Belly Blech Worm is a drone of somekind, created from a fragment of Cackletta's lifeforce itself, similar to the Puchi Ooguras from Densetsu no Stafi 2. the worm in Japan is called the Geragera Mushi (ゲゲララ虫), the Cackle Worm, whereas Cackletta's name in Japan is Geragemōna (ゲラゲモーナ). it's plausible that Blech Worms were dubbed as such because there wasn't an inherent context outside of another laughing-based onomatopoeia like all other Beanish characters and locations, only the Italian translation kept some comparison between the Worm and Cackletta herself. If future games in the series needs to have a boss arena of some kind, they can always have it assume control over Midbus, Popple or even Bowser himself if they want to empower him further than the Mario Brothers affecting his body on the inside during Bowser's Inside Story. if it's anything like the Kirby series, chances are they might reintroduce characters for the sake of fanservice, even in Dream Team Bros, Bowser Jr was introduced into the series by the battle ring, before that there was a throwback in Bowser's Inside Story against a few Shroobs that were still frozen under Bowser's Castle
If Superstar Saga DX has a Battle Ring, the Bonus Boss will be Bowser & Bowser Jr.There are a number of reasons this could happen.
Bowser himself doesn't have a normal fight. His only fight is a tutorial fight and then he spends the rest of the game either with amnesia or possessed.
Every Bonus Boss has been Bowser related thus far (Bowser Jr. and Dry Bowser)
It would give Bowser a bigger role. Bowser is pretty much the Butt Monkey of Superstar Saga (as noted above) and since Bowser's Minions takes place during the events of the game, the mode will probably end when the Koopa Troop meets up with Bowletta. However, making Bowser the Bonus Boss would give him time to shine.
For reasons explained above, Junior is unlikely to appear in Bowser's Minions, but they still have sprites they can use from Dream Team and Paper Jam.
Popple has a fight with Birdo, so he does not necessarily need Rookie. Probably not necessary to point out, but both Mario & Luigi: Paper Jam and Mario & Luigi: Bowser's Inside Story removed Bowser's fights from the medley when he was the final boss (though in the case of the former, it might be because of their tie to the final battle. The same might happen with Bowletta, which would leave Bowser open for a fight.
And finally, teaming him up with Bowser Jr. would allow him to use the gimmick of the later Popple fights: The usage of Bro Attack equivalents.