I still like the version of the "Clone Wars" hinted at by Zahn in the Thrawn trilogy way better than what we actually got from George Lucas.
I do think the clones should have been "the enemy", because wars are typically named by the winner after the party they were fighting
against. The USA fought the (then-known-as-the) Mexican War, and the repeated wars against Native Americans were called the Indian Wars. The wars now called the Anglo-Dutch Wars were called the Dutch Wars by the English and the English Wars by the Dutch. And obviously the Greeks fought the Persian Wars against the Persians, and the Romans fought the Macedonian Wars against Macedon and the Punic Wars against (Punic) Carthage.
Clone Wars, logically, should be fought
against clones.
Failing that, an alternative is to have both sides use clones extensively -- making it the defining feature of these conflicts.
Which is another point: conflicts, multiple. Clone Wars is plural. What we ultimately got was a Clone
War. I was expecting a series of wars, covering a longer period. Zahn also often mentioned it as "the Clone Wars period", as if it was a whole historical era.
Of course, Lucas gave Zahn his early ideas, which put the end of the wars 10-15 years earlier. I think you could easily paper over most issues by actually having there be multiple clone wars over a period of several decades, fought by the Republic against one or more external foes -- that should then rely on clone legions to actually endanger the (otherwise overwhelmingly vast) Republic.
This can also be used to reconcile multiple accounts of who the baddies are. You can have wars against renegade "clone masters"
and against expansionist Mandos using cloned "supercommandos".