I did not want to read every post so i skip many, or should I say everything, so I don't know if you have a story but here is a idea:
Marios cousin Branio kidnap Peach, but Mario doesn't know it was him. So he Suspect Bowser. So after a few level and boss you meet browser and when you meet and defeat him he says that it wasn't him, but he says that he heard it was Branio or something. And he say that Branio is a evil science man, and he can help you to rescue Peach. Then you can choose to be Bowser when you play, and the enemies are cyborgs. and the boss are Branios subordinates. and when you meet Branio you fight him but he is very easy, and when you defeat him bowser comes and eats him(Branio) and then Bowser becomes a very hard boss . and then just defeat him and you are finished with the game.
I wasn't so detailed, and it is just a idea, but if you like you can let those who should the story to make the detail.
And I already said that I didn't read the post before, so don't expect something.