Masiakasaurus
My character is bad at CHA-based skill checks and has a low Will defense. My low stat already has mechanical repercussions. Why do I need to be further punished?
A 10 Charisma is average, and I wouldn't bother penalizing such a player.
However, if a character had a Charisma of 4, in order to have a maximum in several other stats, yet the player kept playing the character as smooth and dapper, or described them as "good looking", I would have a talk with them.
Conversely, if a character had Intelligence as a dump stat, and somehow the player had their character recalling extensive amounts of information about creatures, without making a roll, I would have a talk with them.
When your character has an obvious weakness, play to it. Perhaps a character with low Charisma is horridly socially inept. Perhaps the character has odious personal habits, abysmal hygiene, or maybe the character looks like a cross between the Hunchback of Notre Dame and the Toxic Avenger.
Characters with weaknesses are, in my opinion, infinitely more interesting than Mary Sue characters. Just remember to play the weakness.
I also encourage
"Character Motivations", things that a player sets forth as what drives their character forward and gives them focus. If a player made a character with a low Charisma (for example), and one motivation was to overcome their handicap, by having their character learn social customs, grooming habits, etc. I would reward them with additional XP when they took steps toward overcoming their weakness. In Chaos 6010, these Cool Points (XP equivalents) would only be spendable on Charisma (or Physical Beauty, or related mechanics).