I was thinking along these lines too.
First, I was thinking about rolling a random personality and put it in there. Either let the Player play it or let one of his comrades at the table play it (for the Type B of the Pair).
Then, I was thinking that I could just let one head be dead or Dumb in the literal sense of the word. That seemed sort of boring.
Finally, I thought about actually going your route, which I am glad you brought up. The creative side vs the science side. Probably make for a laugh or two.
With regard to the minuses, this question was spawned by the Ettin's Spot Bonus, which is as a result of having 2 heads (or partially so). So, I am trying to reconcile how I would deal with this.
Instead of a penalty AFTER the change (which is workable), I was thinking of increasing the DC of the check necessary for polymorfin'.
Thanks!