I didn't mind the animation in TAS, but I'd love to see the music redone. I really felt at the time I first saw it (first run as a young teen) and even today, that the music just didn't do anything for the show and took away from it.
Also - I'd have someone else do young Spock in Yesterday. The kid who voiced it did so with a whiny voice.
Some of TAS (like Yesteryear and the Tribble ep) was really good and holds up pretty well. I wish some of it could be converted to live Trek.