Actually, the Bowser levels were always my favorite too. They just seem more "classic Mario" style then the rest of the game. It's how one would expect a 3D version of Mario Bros. 3 or Mario World would play.
The Bowser levels are a very cool and subtle mixture of classic Mario stomp'n'romp gaming with the ever wacky third dimension to make things more interesting. Sort of a 3d platformer on rails. The StarFox games are like this too. Sure, you're in 3d space, but your range of movement is limited.
The inside of the volcano and Rainbow Ride are like that too. Who knows? Maybe, if we're lucky, the next 3d Mario game will be set up like the Bowser levels. . .