I think it would be cool if you didn't even see lower level monsters like that. In the case of CoH, it could even be taken a step further.. Once I complete the Skulls missions, the game could hide all the Skulls thugs and not even show them. Then I could feel like I actually did clean up the streets and make the world a better place.
Maybe it shows them only when engaged in combat by another PC, or when grouped with someone who hasn't completed those missions. I guess it'd be tricky, but I bet there is some sensible way to do it.