These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Better on DVD: Considering the original 4 minute segments, it merges well into a wall-to-wall hour long movie.
Epileptic Trees: Some people play the entire series as propaganda films made by a brief character in Windu's episode. Said character did canonically make pro-Jedi propaganda during Palpatine's reign and his entire backstory began as an excuse to explain the inconsistencies in Jedi portrayal between the show and the films, which some fans had complained about. So it's somewhat implied in his backstory that these are his cartoons, or at least are very similar to them.
Ensemble Darkhorse: Captain Fordo, the Badass leader of the ARC troopers. This series also made General Grievous into one for the entire Star Wars universe.
Villain Decay: General Grievous post series. Grievous was introduced to the Star Wars Universe via this series, but before his character was fully developed for Revenge of the Sith. Whereas Clone Wars introduced Grievous as an unstoppable killing machine who was able to take down handfuls of Jedi without much trouble, the third film had him him behave more like an old fashioned moustache twirling villain who ran away when outmatched. This continuity error was fixed by having Dooku tell Grievous that he must only confront Jedi directly after they are exhausted from battle so that he will have the edge. This fit well with the circumstances of his first appearance.
And, in his last appearance in Clone Wars his entire chest cavity was crushed by Mace Windu. Considering the fact that all his vital organs are contained in his chest, it's more surprising that he lived.