I don't think TCW series made me appreciate the prequels any more. In fact, because TCW was very good (despite a few groaners and other face palming moments), it made me dislike Episode II even more.
I don't think the TCW animated movie was ever supposed to be a stand alone film, but rather a compiled story arc introducing the series as a whole.
I really liked the expansion of characters like Plo Koon, Kit Fisto, Evan Piell and other Jedi masters that were only briefly noticed in the movies. Without seeing TCW, their deaths (or absenses) in ROTS weren't meaningful at all. But getting to know them during TCW actually made me feel something when they died. Actually, I felt they needed more screen time and feel cheated by the minimal death scenes we got. The most impactful death in ROTS, for me, was Ki-Adi-Mundi, we got to see the understanding of the betrayal in his eyes.
So, in some ways, ROTS was improved by TCW, while AOTC felt worse. Not much of an impact on EP I either way, other than knowing that Maul survived getting sliced in half a dropped down a reactor core.
From The Lost Episodes, I am glad we got to see how Boba got the dented bucket, and the fate of Cad Bane, presumably.
Things I didn't like about TCW are few, and can generally be written off as appeals to the younger, targeted demographic. Primarily, every alien species seems to speak basic (aside from Wookiees and a few others). Bossk and the other trandoshans should have been subtitled.
Ziro the Hutt was one of the worst things, as well as the Zillo beast of Malastare. Whatever happened to getting that thing cloned, anyway?
Some of the obvious story arcs getting split up and spread out over various seasons never made sense. The series started with Yoda brokering a deal with the Toydarian king, getting nearly foiled by Ventress. But then, like three seasons later, the follow up of that had Savage Opress killing the Toydarian king in retaliation. I think there was even another part of that arc elsewhere in the series that didn't mate with either episode of the arc. It's only noticed when binge watching. But that's what I did since I was overseas for most of the run of the show.
I loved Rex, though I dislike the retcon of putting him in the Endor commandos, though that was a Rebels thing.
I loved the clones in general, from the training of Domino squad, to their crappy posting on the Rishi moon, losing Droidbait and Heavy, seeing Fives and Echo being promoted to Arc troopers, the death of 99 during the battle of Kamino. The Umbaran story arc and the betrayal of General Krell. And ultimately, losing Fives. The clones had so many good story arcs. Even the crappy D-squad arc got us the Clone Commando Gregor.
And of course, Karen Traviss' books were done of the best things the EU put out. So bummed we never got that last book.
Overall, I think TCW series was the best thing to happen to Star Wars since the OT, though I'm a pretty big fan of Rogue One, also.
I eventually need to buy the series on DVD (or Blu-ray if it ever comes out).
