The reputation per faction/region seems a good idea as long as you don't get too much different factions/regions. It would also make more sense than an overall fame-rating.

Something else that popped to mind: what about hiding your identity and temporarily altering your reputation with certain factions? would you be able to dress up as someone? IE kill a guard of a city where you are hated and chased by the citizens, take his raiment and be able to move through the city whitout being recognised, some citizens might even come to you with a problem. If you take off your raiment, you're cover would be blown, resulting in being chased again.

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