Bowser isn't supposed to be taken seriously as a villain. The entire series is not to be taken seriously.
Thank you, gamers are too obsessed with wanting ALL games to be this very specific definition of "epic" that they fail to have fun - just trick themselves into thinking their having it because of "cool cutscenes" and "great voice acting" and "epic stories". Bull ****, not every game has to fit into this. Mario being the prime example.
The sole point for Mario games is to be fun, whether it's an original style throwback like the NSMB series of games or the 3D platforming series that have been evolution's of Mario 64.
The only reason those games have a story is because is because they're no longer side-scrolling and a story is a way to tell the player "this is your goal". I don't remember there being any story in NSMBW but anyone from age 5 to 105 can pick up the controller and realize "I can't go left, so I must have to go to the right" at the start of any given level. Whereas in something like Mario Sunshine or Galaxy (which is a GREAT game and how dare you not play it!) have open worlds and the story is basically telling you "hey, do this so you can go and do that eventually" Take that away and you're still having fun, aren't you?
If you're playing Mario Galaxy because you really felt the universe was going to be destroyed and you were it's last hope, you're doing it wrong.