Nintendo was already being lazy when they made this game, either they got even more lazy toward the end of the game, or they forgot that bowser's castle was already in the sky in the first paper Mario and in superstar saga
Bowser's Castle didn't float in SMRPG. It was on top of a large cliff.
You're probably thinking of the Weapons Factory, which was hovering over a void. Speaking of Bowser's Keep though, I was disappointed that the section you can access on your first visit was twice as large as the whole thing in SS.
I wouldn't have been opposed to it flying if there had been anything but Bowser and Kamek inside. The last three PM's have had giant final dungeons with epic music big enough to span a whole chapter, but SS just had a 3/4 hall that was probably supposed to look like the entrance to Bowser's Keep from SMRPG, a scrolling carpet, and Bowser (SMRPG had the entrance hall, terrapin room, lava room, and Bowser). It didn't have any music either, just some quakes that would have reminded me of the tremors in Castle Bleck if there had been any logical reason for them to be there.
The whole plot was just PM64 minus any dramatic tension that PM64 had, since PM64's theme was growing more powerful to take on Bowser in a rematch, and this game dumps the power part for "lol health upgrades" and ditches "Bowser is a gloating villain that refuses to be beat ever again" part in favor of "Bowser is shiny".
Tissue to the extreme! For the last time, it's not innuendo.