Take Paper Mario, for example. Bowser could simply take the star spirits and keep them with him up in the castle insted of spreading them areound to places Mario can go. Or he could, with the star rod, kill Mario once and for all. But what fun would the game be if you started and the game said, "Hey, this was a waste of your money because, if you haven't noticed, Mario has been dead before you even loaded the game!."
"There are no such things as stupid questions, just stupid people."