Under the assumption that Charisma basically only affects shopkeepers and companions I suggest the following changes to make the attribute a little more interesting/valuable:

1) Let the requirements for certain quests and tasks partially depend on the Charisma attribute. Examples:
- To join the Thieves' Guild a character with high Ch would only need to apply pick pockets a few times while an uncharismatic character needs to work harder
- Thrundarr might be more inclined to assign very common monsters to high Ch PCs in his first quest while you might get more Shadow Trolls or will'o'wisps if you're uncharismatic
- The level requirement for the Assassin Prince to give the Flik quest might to some extent depend on Ch
- For some situations where a quest is only assigned to characters of certain alignment, a very high Ch might remove/reduce the requirement
- Hawkslayer might agree to join a PC with high Ch even if the original level requirement is not met and might perhaps not want to join a low Ch PC at all

2) Let the rewards for quests be affected by Ch, where it makes sense. Examples:
- Add another modifier to the initial skill value whenever a skill is taught by an NPC that depends on Ch to reflect the enthusiasm with which the NPC teaches
- When (semi-)random items are given as reward, high Ch PCs should get more items and/or items with better quality
- Ice Queen will maybe give a potion or two more to high Ch PCs and less to low ones.

3) Misc marginal stuff:
- Peace offer results should depend on Ch
- The casino guards will allow PCs with high Ch to leave with more of the winnings

What do you think? I personally completely ignore Ch in all of my games as it works now, which is a bit sad.