I was watching someone stream this game... and it really does feel off. The main characters are giant shitstains as noted. massive hypocrites. sociopaths.
I'll admit, I was one of those hopping on with sr3. and having not played sr 1 or 2. SR3 definitely hit a "loveable rogue" tone. they are criminals and hurt people. Buy iirc, none of the missions specifically had you going out and murdering innocent civilians, or good cops. They had you going after rival gangs, and dirty cops/military. you COULD kill civilians, but it wasn't specifically part of the plot or game mechanics.
This game does. Repeatedly you are sent out to kill innocent people. Assassination missions, where you murder innocent people for criminals.