What Could Have Been: The author revealed that there were several versions of Fallen Kingdom to never see the light of day.
The first version was going to be ten books long. There would be no time skip and Mario never died. In it, Morton Koopa would be revived and all the characters would come to together to stop him. The Seven Stars board of directors would have been different, including a prototype for Cobal named Dinor and an anthropomorphic dragon who would have been related to Bowser. Morton and Antonio would have ended up having a rematch at some point during the story. In the end, it would have been revealed that Dimentio was behind everything and was after the source of the Shadow Queen's power, the Grand Dark Star. Mario was going to get the Grand Light Star and fight Shadow Dimentio in the climax, who would be killed when Bowser rammed the Comet Observatory into him.
The second version would have been called the "Mario Finale Trilogy" and would have been split into three books. This time, Skallz Fortiscule would have been the villain and would have been revealed to have been working behind the scenes since King Morton's time. The reason for this was that he was actually thousands of years old and a koopa prince, who was passed up as an heir for not having dragon-koopa genes. He had also split his soul into several different versions of himself. Antonio would have sacrificed himself by ramming his battleship into a god like Skallz in the climax, and it would, again, end with Bowser's sacrifice. The idea was scrapped for being too confusing.
Within the current story, there were other confirmed ideas that were scrapped
Yoshi was planned sacrifice himself by ramming a fighter plane into General Flame's warship. This was cut because the author didn't want Yoshi to die while the world still knew him as the guy behind the Neon City bombing.
Ludwig was going to revive dead foes of the bros and have them fight for him.
Billy, the yellow toad from the Toad Brigade, was meant to be one of the main characters in the story. This idea was cut because the author couldn't come up with a reason for him to be with Luigi and Cobal.