I think your reputation should have a large impact upon how people react towards you. For example if your are a very infamous character then you would have large price on your head. Bounty hunters, law inforcment, etc... wouldn't just attack you out of the blue, they would capture while your resting or something. Then you would put in jail, kinda like at Junktown in FO 1. You would be either sentenced to a term or to death. Either way if you have a high sneak and lockpick skill you would be able to escape...eventually. Hell, they could even go as far as to set up a Jail town place on the map. A place where the law inforcement agencies across the wasteland could put their prisoners.
Also, I think weaker people who retreat during combat shouldn't be considered hostiles after combat is ended. I mean if your engaged in combat with 4 enemies and one retreats and you kill the others then I think the one left shouldn't be considered an enemy. This way when you start a fight in a town you won't have to kill everyone in the damn town. It would almost be like taking over a town.
Also, I think weaker people who retreat during combat shouldn't be considered hostiles after combat is ended. I mean if your engaged in combat with 4 enemies and one retreats and you kill the others then I think the one left shouldn't be considered an enemy. This way when you start a fight in a town you won't have to kill everyone in the damn town. It would almost be like taking over a town.