Well, in my story this isn't some simple power struggle between two guys over a princess and her castle. Bowser kidnaps Peach because he wants royal blood to breed his descendants. and he is trying to capture the Mushroom Kingdom is because Castle Mushroom, the castle from Super Mario 64, is an inter-dimensional gateway and he plans to use it to conquer the entire universe.
Mario is trying to stop him because he plans to conquer all of the universe, not because he kidnapped a girl.