This Mytoons article by Rusty Mills, about unused artwork and develpment for Animaniacs reveals that the Ben Stein character in the cartoon "Chairman of the Bored" (co-directed by Mills) was originally drawn as a dog. In the final version, the character, who won't stop following the Warners until he's finished telling them his entire rambling story about how he met Bob Barker, was a human. A few Animaniacs cartoons actually had them going up against humanized animals, like a bear who owns a house and a garage in "Garage Sale of the Century," and it never worked quite as well as having them interact with humans.
Although the three lead characters on Animaniacs were not exactly animals -- they were supposed to be animal-like characters with no particular species like some of the early imitators of Mickey Mouse -- they were clearly characters who functioned best in a human world, because they were supposed to be the only crazy characters in a world that otherwise takes itself seriously., and because their behavior only made sense if their antagonists were the kind of people we'd like to see taken down a peg in real life (in other words, humans like the ones we know).
But another character on the show, Slappy Squirrel, was just the opposite; she was at her best in cartoons where her antagonists were cartoon animals (dogs, wolves, chipmunks). Her specialty was taking delight in inflicting violence, often without provocation, and demonstrating her knowledge of cartoon conventions; that often seemed too cruel and nasty when she was up against a human, whereas inflicting violence on a cartoon animal seems less harsh. (That's why Wile E. Coyote can take more of a beating than a human like Elmer Fudd or even Yosemite Sam; there's a limit to how much you can hurt them without the audience realizing that there's a human being there, even a cartoon human being, getting sliced in half or squished.) Though the one where she was fighting Daniel Boone worked very well, so there goes that rule. The point is just that whether a cartoon uses a human or animal antagonist is a tricky question that depends on the nature of the story, the characters and the conflict.
