Well the only one off the top of my head is that Grevious, for the most part, is much more formidable than his 3D Clone Wars counterpart.
Although no longer canon, I always thought how the two shows fit in quite well if you think of it this way:
2D Clone Wars (Season 1) ->
3D Clone Wars (all seasons) ->
2D Clone Wars (Season 2)
Season 1 has Anakin right after Attack of the Clones as a padawan. Still very immature, rebellious, whiny and has the same hair style. Once he deafeats Ventress and matures a bit more after learning his lesson, than his personality and looks changes more to his 3D/Revenge of the Sith appearance.
Then you jump to the 3d series. He trains Ahsoka, goes through all his ordeals for the entirety of the 3D Clone Wars Series, and then after Ahsoka has left the Jedi Order you have 3D Clone Wars ending, and you jump right into season 2 of the 2D series and it surprisingly feels natural since Ahsoka is gone, and leads right into Revenge of the Sith.
The only problem is Dave Filoni has already mentioned how the events right before Revenge turn out differently than in the 2D series, with Anakin instead lending Rex and some of the 501st to Ahsoka to help liberate Mandalore, complete with custom Ahsoka painted clone armor as a surprise and then he leaves off to help save Palpatine.
That alternate take by Filoni is kinda pseudo canon just because we have not seen it happen in any form of media yet. Personally, I think it is a bit much, with the whole Ahsoka themed clone troopers and freeing Mandalore from Darth Maul thing, it just reeks of fan service to the highest extent. Like why is she leading a clone army after leaving the jedi in the first place? I dunno, I always preferred the 2d series so maybe I am biased.