[Warning: What I am about to describe is something that, if made, I would want to be a part of the main series. But since in the unlikely event it is made, they'll probably make it a spinoff, I'll post it here]
Super Mario Ultimate: Starts off as your typical Bowser-kidnaps-Peach story, but the first world spans the entire Mushroom Kingdom and after beating Bowser at the end, things take a turn for the rather dark. It is revealed that Bowser was being controlled by a greater evil who has taken over the Mushroom Kingdom, along with Sarasaland, the Beanbean Kingdom, the Sprixie Kingdom, Delfino Island, Yoshi's Island, and Pi'illo Island. Peach is revealed to possess a treasure that, combined with treasures found in the other realms, are the key to opening the path to Rainbow Road, the final world where the new mysterious antagonist has created his dark castle. The major bosses are: Bowser (World 1), Tatanga (World 2), Fawful (World 3), Hisstocrat (World 4), Bowser Jr. (World 5), Kamek (World 6) and Antasma (World 7). Mini-bosses include Boom Boom (World 1 Tower), Wario (World 2 Tower), Popple (World 3 Tower), Motley Bossblob (World 4 Tower), Petey Piranha (World 5 Tower), Boshi (World 6 Tower), Smoldergeist (World 7 Tower), and Dimentio (World 8 Tower)
Each boss and mini-boss is set free from the control of the main villain once beaten. During the final battle sequence, they all join together to wish on the stars for your victory, in return for freeing them. The credits music is a remix of Super Mario 64's credits theme, and during the credits the residents of each world are shown repairing all the damages made by the takeover of the main villain. In each sequence the characters will wave to Mario and Co. as they fly by on the pink airplane from Mario Sunshine. In the last segment of the credits the main villain is shown, being humiliated in some way.
If you dislike this idea just bear in mind it took me about 10 minutes to think it up so it's not perfect.