From what I've heard bad in Saints Row the Third, is that sometimes the weapon selection screen is kinda clunky, and that the weapons don't really have much different, like a sub-machine gun doesn't feel much different than an assault rifle.
Also one thing which I heard that makes it bad is more of a personal thing, is that it can breach your moral standards. Like I think at one stage you have to go and rescue prostitutes who are trapped in steel storage containers with fisting machines, and sometimes you have a moral standard which you live by. Also the fact that you can hit people with a giant purple dildo, is more foul than funny for some people.