^_^
well, the clone wars; by implication of the name, the clone wars could be about the abuse of clones as infantry, and yeah, order 66 would still happen, so just replace the droids with clones in different armor.
the scene of yoda vs dooku, where dooku has the reactor thing fall on obiwan/ani; instead of simply letting it drop, yoda should have had a crowning moment of badass and thrown the reactor into dooku's ship, causing it to crash, clones capture dooku, and thus deliver a crippling blow to the sith and ending the clone wars alot sooner.
one interesting irony is how the in-universe mandalorians of that era side with the seps, leading the clones to despise their mandalorian heritage (jango), and eventually drop it in favor of more generalized Imperial Culture. i would change it so that there would be both jedi and mando generals and commanders.
i also would have had the ARC-170 pilots helmets more enclosed, with the visor screen covering the whole face, even tho its transparent. that way you get a more sensible continuity to the rebel and tie fighter costumes.
i also would have up-powered the jedi and siths force abilities, but then again, im a fan of TFU