I'm not sure it would be as hard as your making it out to be there. The companion responses could be in line with your characters current alignment leaning (and could come from their already populated voice catalog of responses). As stated by the original poster and many since, the alt you "companionize" wouldn't be earning xp so its not really a quick leveling scam. I would imagine your skill options would pull from either your most used skills or defining character skills (my sawbones main would primarily have his healing skills, my vanguard would primarily have his taunt based skills). I actually think allowing the companion to have access to all their skills would make it unreasonable to coordinate as a companion, but allowing them access to their higher level skills would reflect the nature of the relationship between the companions (e.g. if my smuggler was level 50 and my trooper was level 20 the smuggler should still have his ship callin skill even when he's acting as a 20th level companion).
I like it, its simple (relatively) and really gives the legacy system a feeling of family implementation. You could then have that epic family moment when Darth Vader turns on the Emperor to save Luke. Now really, now amazing would that be?