I can't be the only person who hated New Vegas's reputation system... I mean, I guess I'm fine with the concept on paper, but in practice I didn't feel like it added anything to the experience. Between disguises, mixed reputations, and psychic NPCs (being undetected when killing someone not being enough is stupid) and how all of those parts work together just doesn't feel like it makes logical sense in the game world, and I hated how inflexible it was.
Not to mention the wonderful phenomenon of the Legion sending death squads after you at the smallest amount of negative rep, and then you inevitably become vilified after that for killing their Legion assassins. Or getting locked out of the Powder Gangers quests (which are the only way to actually side with the NCR and take down the Powder Gangers) by killing anyone during the Ghost Town Gunfight quest, since it counts your Powder Ganger kills on top of the reputation hit just from completing the quest.
I'd much rather something like Skyrim's regional bounty system, but organized by factions instead of by geographic regions.