The penguins, the catipillar, Eyerok talks like he's been there for centuries, the underwater town in Wet Dry World seems like its had some background, Koopa the Quick, a sign in Jolly Roger Bays cave suggests pirates used to be there. The Bob-omb buddies sole purpose is to open the cannons, and the only cannon outside the paintings is the one near Peach's Castle, but that one has grating over it, not the Bob-omb Buddies metal plate with their picture. The Bob-omb King talked like he's always ruled over the battlefield, and the official guide says the Pyramid is ancient.
I think the only places Bowser really made where his levels and added some traps to the other levels.