I always imagined the Clone Masters were geniuses of genetic engineering; throwing supersoldiers, war beasts, etc. at the Republic forces.
An alternative idea I toyed with years ago was replacing the Trade Federation with the Clone Masters as a powerful semi-independent faction within the Republic. Maybe they supply the Republic with it’s troops (like in the PT) and then try to stage a coup. Meshes with the PT a little better.
I also toyed with the idea that the Mandalorians are creation of the Clone Masters, but I prefer them to be technologically advanced warrior nomads like in the old EU. Hell, maybe the Death Star was their idea.
Are we agreed that Leia definitely gets a red lightsaber?
The Force extends ones life - I always envisioned this. So, Obi-wan is around 100 years old in Star Wars and had fought in all three Clone Wars.
The devastation of The Republic after the Clone Wars is what leads to Palpatine taking over. The various large Guilds (Transport, Power, etc.) get him elected, thinking he is just a useful idiot and would make an ideal figurehead. He turns the tables of course.
EDIT: Episode 1 drops us into the middle of the last, and most devastating, of the Clone Wars.