Oh, I've seen enough to know that not the whole game takes place inside Bowser, but it just seems like it from all the screenshots and other PR stuff. At least, I think so--it always bugs me when stuff like the Bridge to Terabithia movie make you think that the whole thing is about a relatively minor aspect that sounds cool in a trailer.
Also, as far as I can tell, the inside-Bowser parts are 2-D sidescrolling. I say that's a good way to contrast between it and the rest of the game (also, I'm psyched for the sideways, touch-screen-using Bowser battles).
Also also, for purely cathartic purposes, with no intent of Nintendo-bashing, and in a not-all-that-serious manner, here's (in no particular order) every other form of media I can think of that has explored the story hook in question to some extent:
Videogames:
--The Legend of Zelda: Ocarina of Time
--The Legend of Zelda: Oracle of Ages
--Super Mario World 2: Yoshi's Island
--Mario and Luigi: Superstar Saga (technically)
--Mario and Luigi: Partners in Time
--Okami
--Gears of War 2
--To some extent, Star Fox Adventures and whatever (games) it was where you go inside a robot to destroy it
--The Contra series
--Life Force (AKA Salamander)
--Paper Mario
--Super Mario Land 2: Six Golden Coins
TV shows/movies/books:
--Multiple SpongeBob episodes and some Fairly OddParents/Jimmy Neutron episode
--This one Honey, I Shrunk the Kids TV show episode I saw when I was younger (did anyone else watch that show?)
--The Fantastic Voyage Adventure and Through Inner Space (or whatever they were called--but that's a given)
--At least one episode of The Magic School Bus
--Pinocchio (both the movie and the book, I think)/Finding Nemo (to some extent)... and, of course, the story of Joseph and the Whale is probably what started it all.
Of course, the main difference here is that Mario and Luigi are not inside Bowser to kill him or cure any medical conditions he has. Still, I do worry that the game will be predictable in some spots... and if at any point I have to make him sneeze to get out of his body, I swear I might just turn the game off right there.