While the companion system is really nice to have, especially compared to other MMOs, I think the restriction with them being removed from changing hairstyle, using collectibles like head markings etc. supposedly to keep their "identity", is questionable. Even more so with thousands of clones running around.
I think if you want to keep the identity of a character and still allow players not only to customize that companion but also be more enticed to collect appareances from the game (in-game reward, store, crown crates), we could go with one the following suggestions :
- Daedric possession
- Soul transfering, such as a powerful mage or ritual transfers a soul to a new body, either willingly (e.g., to avoid death) or forcefully (e.g., body hijacking)
- Memory Transfer (Sotha Sil–Style)
- Ideal Master Pact, the cursed Soul Cairn Bargain
- Time / Reality Manipulation by the Psijic Order
- Shaping Reality (Sheogorath shenanigans)
You would get a short questline with a dialogue option to choose which character you want to use as reference.
Then, if you want to change, within the dialogue/companion menu, you'd have the possibility to select another character.