It's the main issue, that magic is far to weak, mainly because the armor system screws mages far more then warriors. Because of their elemental effects magic deals less pure damage, but elemental effects are hardly important, as long there is still armor left. Also only magic is at current state ainfluenced by resistances. That is why a pure physical team will have less problems in fights than a pure magic team and I guess polymorph made this imbalance even worse.
Does not sound as if they changed Battlestomp. As far as I remember Battlestomp was never affected by weapon only by level, STR and Warfare, because the attack gets done with your foot (stomp). And that is why a staff won't change the type of damage.
