Being able to rape everything is fun for a while, but after doing it for hours on end it gets boring. If the player ends up being so powerful that he can rape everything without consequence halfway through the game, the player should be meeting more powerful enemies to match his power. Ie. if the player becomes a demi-god, he should be facing demi-gods. Being all-powerful is incredibly boring when there isn't any competition.
Or there should be more of the weak enemies and they should have abilities that allow them to be more effective in large numbers and/or support a stronger 'leader' enemy. Then you get the best of both: killing enemies by the dozen and you still have a challenge.