All this talk of TCW makes me want to revisit it and see if it holds up as well as I remember--and more importantly, how well it stands against the Clone Wars Multimedia project, the majority of which I haven't actually read through. Maybe after I run out of post-Endor stories to give my lengthy impressions on, doing reviews of the Multimedia project and then an arc-by-arc coverage of TCW for comparison is something I can tackle next (except for TCW Season 7, which isn't canon to the EU).
That is, if anyone is even remotely interested in reading that. I know that my perspective would likely clash with a lot of people's here.
When it comes to comparing TCW with the Clone Wars Multimedia Project, the latter has more range, since entire comics and novels and games can focus on any given character or topic, but TCW has more narrative unity, since the same crew is working on all the episodes. The Clone Wars Multimedia Project has a great library and expanded upon many of the characters, but storytelling and character portrayals were kind of all over the place: some works like the 2003 Clone Wars cartoon and the Republic comic series treat the Jedi as the good guys and have people praising them while they show off neat powers, other books have the exact opposite and demonize the Jedi while praising someone else as being better, ie. the Republic Commando novels.
Some characters can also have varying depictions: Grievous in the 2003 cartoon was known as "White Vader" by the fans because he was so good at killing Jedi and was so badass, yet in the Labyrinth of Evil novel, Sidious casually mind-rapes him in a conversation. The Jedi are depicted as caring generals who love their men by one author, then they are depicted as amoral dickheads who use clones as suicide soldiers by another author. In works like Galactic Battlegrounds, Jedi generals like Sev'rance Tann and Echuu Shen-Jon were military masterminds, in the Republic Commando books, they're failures who don't even deserve to command a parade, let alone an army. Taken together, it's kind of a mess. A pretty entertaining and beautiful mess, but it was still kind of a mess.
Meanwhile, TCW mostly has a unified vision and message. It was more childish at times, nerfing some of the characters that had near-godlike combat skills in previous works like Grievous, but in other things, it sometimes did a better job than the previous works.
Take the Mandalorians, for example: The depiction of the Mandalorians in the Republic Commando novels came off as a Mary Suetopia where the Mandalorians are just right, they're the honorable good guy warriors while the Jedi are big fat hypocritical meanies, which ends up wearing out its welcome when the reader happens to have played enough games and read enough books to know that Karen Traviss is talking out of her ass, but in TCW, you have two groups of Mandalorians who have decent, understandable reasons for their ideologies: the Pacifists saw how previous conflicts between Mandalorian warrior clans has sapped the planet's strength, and so they wished to pursue a peaceful path of economic development that would gain them soft power when it comes to politics, while the Death Watch are true believers in the Mandalorian warrior ways and they have legitimate grievances concerning the pacifists stomping all over Mandalorian traditions that are thousands of years old. Neither side is perfect: the Pacifists don't use their economic strength for military purposes, which makes it easy to plot against them, and there's way too much corruption in their ranks, while the Death Watch are assholes who murder civilians on a whim, and outside of Maul coming in to advise them, they couldn't even conquer a planet ruled by pacifist hippies. But they both had advantages, since the Death Watch warriors are some of the best, and the pacifists have a lot of friends outside their own domain, from the neutral systems to the Jedi Order. That's a more nuanced take on the ancient warrior race than just having them be a Suetopia while the author spends more time shitting on the Jedi rather than actually showing the kind of Operator shit that Republic Commandos should be doing.
However, TCW also has its flaws, especially in terms of focus. Since there's less material than the old Clone Wars multimedia project, we can't get enough focus on characters Filoni doesn't care much about. Characters like Shaak Ti, Aayla Secura, Quinlan Vos, among others, deserve to be more than just cameos. Instead, Filoni has episodes like smugglers who fail at smuggling or some little people stuff instead of putting in episodes concerning Delta Squadron or some other Jedi. Barriss Offee's fall to the Dark Side was out of the blue.
It also makes no sense in some arcs, especially in the Wrong Jedi arc, where Tarkin persecutes Ahsoka Tano despite the fact that the latter saved his life and he knows Ahsoka is close to Anakin, another one of the Chancellor's favorites. Why the hell would Tarkin persecute Anakin's prized apprentice, when the two of them were portrayed as close friends in the first SW movie? I'm surprised Tarkin didn't get an impromptu Force Choke from Anakin for that. Similarly, the Order 66 brain chips makes no sense, since if that was the case, that they only killed the Jedi because of a trance, the clones would have revolted once the chip's effects wore off. That, and Rex knew about the chips, so it makes no sense that the clones weren't saved from the chips-the only logical conclusion to that story arc would be that the clone commanders and their soldiers all get a weird cut across their heads, and they tell Sidious to bite their plastoid-encased butts the moment he issues Order 66. At least in the old media, nobody knew about Order 66 since EPIII wasn't written yet, and it came as a surprise kick to the nuts when it finally happened.
So yeah, there's my assessment of the differences between TCW and the old Clone Wars multimedia project. My solution to the problems in both is to just pick and choose which parts of both I count as part of my own personal Clone Wars canon.