I am saying this as someone who's played a game of a similar format (though not as animated as yours), and in response to another commenter's comment.
Considering that excess EPs are carried over and to be used in the next location (i.e., a continuation as opposed to fresh start), I'd argue that the current final bosses' difficulty levels are just right. They are after all not the FINAL-final bosses. Perhaps if any adjustment is to be made, maybe it could go into the next stages' development instead, e.g., somehow make the enemies difficult for Stan's natural attributes but easier on Apolonia's.
Well done, Noobilator7! It is an addictive game. In my experience, even my already being familiar with the game format does not take away from the gratification.