The "Animaniacs" special features don't have any input from the artists, at least in the first two volumes (volume 2, to be released later this year, will have interviews with the entire writing staff). Hopefully someone will correct this in Volume 3 and invite some of the directors in to talk about the show, people like Rusty Mills, who would have a lot to say about working on the show. Mills directed the first Pinky and the Brain cartoon, and the look of it was very important to the success of those characters: the dimly-lit laboratory was so different from almost any setting for a kids' cartoon that it was almost a third character in the show.
"Animaniacs" was not, by most accounts, a show that featured a great relationship between artists and writers. On "Tiny Toons," as I understand it, the artists had more freedom to add things to the scripts, throw things out, add their own ideas to the mix. By the time "Animaniacs" came around the writers had grown more proprietary about their material and the two teams -- artists and writers -- more suspicious of each other. I don't think it showed up too strongly in the first 65 episodes of "Animaniacs"; the scripts and the visuals were sometimes kind of at odds with each other (like the way the Warners kept being written as the Marx Brothers while the artists were trying to make them into more cartoony characters), but the contributions were of a very high standard all around. By the time the show moved to the WB, though, I think the seams really started to show; a lot of those later cartoons look dull sometimes, even the ones TMS was available to animate. The show really did become "illustrated radio" at some point.
In the first season, the cartoons to look for if you're interested in the visuals are some of the ones handled by the people at StarToons in Chicago (they did many of the Slappy Squirrel shorts, including the really beautifully-animated "Bumbie's Mom"), and the cartoons done by a unit at WB that included storyboard artists Audu Paden and Carolyn Gair (later Carolyn Gair-Taylor): they boarded cartoons like "The Monkey Song," "Les Miseranimals," "Space-Probed," "Bubba Bo Bob Brain" and "Astro-Buttons," really spectacular-looking cartoons -- no matter which animation studio handled the finished animation -- with great staging of the gags and a real feel of spaciousness in the handling of large casts of characters; it's like TV animation on a grand scale.