Executive Meddling: Shigeru Miyamoto was not exactly thrilled about the addition of story elements in the original game (in the form of an (opional) sidequest about Rosalina's backstory) and requested the Dev team to scrap the plans they had for this game.
One secret star in the Puzzle Plank Galaxy involves you fighting Bugaboom in the exact same way you fought him in SMG1, only with a Palette Swap and with the Cloud Flower instead of the Bee Shroom. The star's title even lampshades this with its title, "Bugaboom's Back". Also, there's a boss rush mode later on in the game involving other SMG1 bosses.
What Could Have Been: It's true that Mario games aren't known for their plots, but it would have been interesting to see where the dev team was planning to go with their story ideas, had they been given the chance.