I don’t consider the 3D series to be in my personal canon because of how much it contradicts Revenge of the Sith, so I’m fine with just having the 2D series and the Republic comics from the early 2000s being what I think happened during the Clone War. Perhaps when I read them, the old Clone Wars books (from 2003-04) will become part of my personal canon as well.
Don’t mistake that I love the 3D show, but I don’t think it fits into canon or legends timelines.