Notice how all the animal sightings appeared in the early episodes, back when a lot of animals were missing from being Pokemon. But now, Pokemon fill just about every popular role for an animal.
I like to think that the major, "large" animals don't exist in the Pokemon world and only minor ones, like insects, small fish, varied invertebrates, and microscopic creatures exist as non-Pokemon. Pokemon are just too powerful for regular animals to compete with them to co-exist.
I've also got my own theories on Pokemon used as food, but I like to think that Pokemon are very rarely, if ever, eaten in the modern Pokemon times. And before you mention the SS Anne episode when they were thinking about eating Magikarp... it's like those old cartoons where two people are on a desert island and they begin to imagine each other as food. Plus Magikarp is usually perceived as being worthless whereas a fish Pokemon like Goldeen is more intelligent and capable in battle, so eating one may seem more barbaric.
