That could work, i was thinking ages ago that someone could re-edit the naboo conflict to perhaps be something to do with the clone wars. alot of wars begin as something else, then develop. WWII for instance started along time before the UK and US got involved.
but i like your idea of there efectively being a Clone Wars I and Clone Wars II perhaps. In the pre-prequel days i always imagined the clones were mandalorians who were the antagonists.