1. More characters and seems a lot more fun
2. More characters involved
I voted SM64DS, but I also think they added some different stuff to the story. People don't have "HP". A good example of is this: http://fanstuff.hrwiki.org/index.php/Stinkoman_20X6:_Reloaded. A comic telling the story of a videogame and seeing if you can find the obvious differences that makes bosses have "three hits" or whatever.
Wait a minute. I agree with son of sons that remakes are more canonical, BUT I do'nt think SM64DS is a remake. I think that 64DS hapenns oh... a year or 2 AFTER 64. How else do you explain 50 new stars, and 3 new playable characters?
Asking why things are different in remakes is kind of moot; the creators are basicly retelling the game, eliminating old story points and replacing them; just because Robirdo was in Super Mario Advance and not Super Mario Bros. 2 doesn't mean its an entirely new adventure; just because there are more levels in Super Mariuo Advance 3 doesn't mean its an entirely new adventure independant of Yoshi's Island.
He did perform a significant military coup de tat of the Mushroom Kingdom in SMB. If Peach did not have the power to undo Bowser's spell, the fate of the Mushroom Kingdom would have been sealed. Also, Bowser conquered much of the Mushroom World in SMB3 - a tremendous feat to say the least. Some may say this was his biggest military victory.