I think Faction Reputation is the best choice especially if there is more than a good side and an evil side..
Which I certainly hope is the case.
Your track record will determine the various factions attitudes and treatment of you.
What have you done for me and mine?
What have you done against me and mine?
Plus how in sync you are with my values and attitudes.
You might be a good person to have in a fight, but if you think civilian causalities are totally acceptable, then some groups will only want to deal with you at arm's reach.
Plus are you a sworn friend or foe (Someone who is committed is held to a higher standard be it committed to your side or to your enemies).
I see Karma as an older game mechanic that should be removed if they can't make good use of it some how in Fallout 4.
Karma could be used as a kind of what you know about yourself stat.
Reputation is what others know about you.
Honor is what you know about yourself.
Or what other whisper about you behind your back.
If people who cross you keep disappearing and anyone who joins you on a treasure hunt doesn't make it back leaving you in sole possession of the treasure...
Well if that happens enough times, then your reputation is going to be questionable even if there is no hard evidence.
Using your karma as an additional modifier to your Charisma could be useful.
Maybe letting a more "paragon" reputation giving you pluses with the more civilized and kind hearted factions and a more "renegade" reputation giving you more respect from the more survivalist minded factions.
Or it could set you up to be taken advantage of or be isolated depending on who you are dealing with.
It would all depend on how this was reflected in game and what differences it made to your Sole Survivor's story.