I was thinking about this today for some reason, but I wonder why Decipher decided that you couldn't replace a companion with a different version partway through the game (like in SW:CCG)? I think it could be a fun house rule: if you have a different version of a companion in hand you can replace the one in play simply by paying the cost as if you were playing them for the first time. All active cost modifiers would still apply. You keep any cards that are already played on that companion (provided they still apply - can't keep a knight weapon if the companion is no longer a knight, etc). And you also keep all wounds on that companion.
It might lead to some interesting decks, or at least some more strategy. Think about replacing
Sam Son of Hamfast with
Proper Poet for a run to site 9. Swap out any Gandalf with
Mithrandir for a beatdown. I'm sure there are ways this could be abused terribly, since they didn't account for it during card design. But what cool combos can people come up with?