Well there is the fact that ObiWan and Anakin appear to have not met Dooku since Episode II, nor have they ever met Grevious face to face. Clone Wars ignored boththose points. Plus the entire Seperatist Council is capturedin TCW despite stillbeing free in RotS. There are differences in the way the politics of the war are portrayed as well.
And this is coming from someone eho loves the show and wishes it had several more years to wrap up its storylines.