Interesting thing is Clone Wars CG overrode a lot of what was assumed Star Wars EU canon as well, including stuff that had come out during the prequel era.
For example there's the whole Mandalorian/Clone troopers thing, in the Republic Commando novels it's made clear that the troops adoped Mandalorian culture and were trained like Mandalorian warriors by Jango and several of his colleagues, there was even an action figure box set along those lines:
https://www.rebelscum.com/tacrefomega.asp
However, Clone Wars just had them be trained by some other guys and Jedi, and that's mostly it.
Also the timeline of the war was that Anakin wasn't promoted to Jedi Knight until fairly late in the war, but the Clone Wars CG and other sources have him elevated almost immediately after Geonosis.
The Separatists are also portrayed as somewhat more dimensional and sympathetic-The Neimodians for example and even part of the Trade Federation itself insist that Gunray is leading a rogue faction; as do several of the worlds and corporations tied with the Seperatists, whereas the earlier EU seems to have pretty much everything be one-dimensional.
Jedi die at different times as well, or don't die at all, in the war.
And no sign of Ashoka anywhere.
In a way the Clone CG series is sort of a prototype for the mostly clean slate Disney made out of the EU stuff.
Maybe someday some of the sequel trilogy EU will have similar treatment? Admittingly the "Operation Cinder" stuff doesn't seem to make as much sense if Palpatine's still around.