Zahn's post OT trilogy of books mentioned that there were clones of Jedi, not just clones of a bounty hunter. Perhaps, one aspect of the Clone War could be Jedi vs cloned Jedi...how would each one know which was the real one, or more to the fact, how do you fight an enemy who knows your exact move as you're about to make it? Perhaps Darth Vader could be born of Anakin's clone...a replacement who genuinely doesn't know that he is a clone and filled with the rage of watching himself die at the hands of his closest friend?
Having the cloned Jedi involved might give more impact to the whole Clone Wars idea, rather than a slightly weak 'we've cloned a billion versions of this one man, let's use them to fight' type thing....