I think It should be easy to implement, and I am playing with the idea of doing it myself, but of course if some talented modder is interested it would be even better. Maybe there is something already modded in this line, if so, please tell me. Or maybe it is already implemented in other TES games (Skyrim is my first)
My idea in broad terms:
After character creation or whenever the player decides to do it you could select some flaws to your character through a MCM menu. Those flaws could be (i.e, could be hundreds of them, and the values are merely orientative):
Clumsy: -25% to discretion and -25% to steal
Stupid: Experience gain is lower than average
One-armed: You cannot use bows, dual wielding, 2H weapons...
Crippled: Your movement speed is reduced by 20%
Taciturn: Speech -15% and experience gain thorug speech is reduced by x%
One-eyed: Archery -25%
As I said before, the examples are just examples, the list could be larger and larger.
After selecting the flaws you should receive an amount of feat points related to the severity of the flaw, the worst the higher the award.
Then, you could invest those points in acquiring some feats:
Agile: +10% movement
Sneaky: +10% discretion
Cunning tongue: +10% speech
Magic skilled: +50 to magicka
Attractive: +15% to speech against persons of the opposite six
These feats could be ranked, therefore the better the feat the higher the cost.
The maximum number of feats/flaws should be fixed, i.e: 3. And for immersion sake, once the flaws and feats were selected and the "design" approved, these would be permanent.
I think this could bring some deep to the characters.