I tend to be bothered by Charisma as an Ability Score. Not just because I see players everywhere dump their lowest rolls into that last ability, but because certain things that D&D does with it just don't sit right with me.
Take for instance, the dreaded Dwarven Charisma Penalty. Yes we're balancing out a racial +2 Con boost, but I have a hard time imagining the Dwarven Race functioning as a Society under this stringent genetic disadvantage.
To combat this, I've borrowed from GURPS in a roundabout way, by using a relative Charisma. Sure, at character creation that Dwarf loses two points to his "dump" stat, and we use this new score for virtually all topside social interactions, but among Dwarvenkind, suddenly that effective Charisma is two points higher.
This House Rule is dangerously expandable though, and I have to exercise as much restraint as possible to prevent myself from drawing up extensive “Social Interaction” charts, penalizing Races according to racial and cultural flavor. Take for instance our Dwarf from above. We’ll give him a Cha of 8 (the effective Charisma among humans), among dwarves it’s an average 10; yet among elves/goblins/orcs it’s 6. Charisma becomes a nebulous score, on paper it’s based on the dominant paradigm of the most populous race (Humans in this case).
Mechanically, Charisma never really seemed to do enough in D&D, although Third Edition has helped a little by expanding Cha based skills and character classes that derive spells from the stat. But unless you're a Cleric (Turning Checks!), Sorcerer (Spells!), Bard (Perform!), or Paladin (Divine Grace!), Charisma is still almost guaranteed to be vying for a player's lowest ability score. Until higher levels that is, when Leadership and Followers start becoming appealing…