This would be magic to me. It never made sense to me that the Rebellion era was referred to as "a great time of civil war", when it was really just a ragtag group of fighters going against the empire. Conversely, the Clone War(s) was a giant civil war with different factions in the Republic battling, but is never referred to as a civil war. Also, why the heck are they referred to as the Clone War"s" when there's really only one war, and only one side has clones? The Clone Wars really needs to be re-defined as a long term series of wars, spanning many generations, fought against an outside enemy (like the Ssi-Ruuk from Truce at Bakura, or the Hapes Cluster from Courtship of Princess Leia), and fought with clones on both sides.
I would recommend taking the info from the Timothy Zhaan trilogy and running with it. Spaarti cyliders are where clones come from (not Kamino), and both sides have them. Clones take a full generation to grow, which is why the "wars" are spread out - both sides need to grow more troops. The empire eventually won because of the discovery that the yslamiri allowed clones to grow faster, giving the empire the winning edge.
One of Thrawns ideas was that fast-grown clones where unstable (due to the force connection). So maybe they did start with generation long clones, but then one side figured out the trick of fast-growing clones, the other side did copy the technology eventually, and suddenly the Clone Wars were in full operation, but at some point, the clones got mad.
The question is - what should the sides be? I kinda like the idea of the Republic turning into an Empire, aided by the War. But maybe instead of fighting Seperatist, they are fighting another galactic government- maybe the (no longer just Trade) Federation or Galactic Alliance. One thing to do would be to reduce the "scale" a little. The Republic is large, but it's not covering most of the Galaxy. The Galactic Alliance has been around for some time and is also large - but maybe not that large. So they are using Droid and Clone armies first. The Republic can rely on their Jedi to fight for them.
The tide really turns once they create fast-grown clones. But thanks to the Emperors foresight, he has his own clone army ready - and this army contains Jedi among its ranks. This is of great concern to the Jedi Council, since they were not aware of this plan. The first batch is still "regualr issue" slow-grown clones, but as the battle intensifies, the enemy fast-grown techology is also stolen. Unfortunately, it turns out that these fast-grown clones are mentally unstable (as per the Thrawn trilogy). So the Galactic Alliance switches to use more Droids, while the Republic keeps using their new clones. The Alliance finally has to admit defeat, and at that point, the newly chosen Emperor orders the destruction of all clones and the Jedi, and issues a ban on most combat and war droids. The public is happy, because the mad clones - especially the Jedi - were a big problem, and almost everyone has had a family member lost to some Alliance war droid.
The Emperor is now in control of all sources of clones, droids and The Force, exactly as he wanted.
But the remains of the Galactic Alliance will form the base of resistance against the Empire once it shows its ugly side.
Of course, this is just the overview - the crucial things happening to Anakin or Obi-Wan are left out so far...
Is there proof of this, because I never heard of it before - even the documentaries never state anything like this.
