Pokemon should exist in relatively small numbers compared to normal animals. Even common ones like pidgey should be something that's sort of rare that you'd have to search for among normal wildlife. Looking back throughout history, certain animals and other strange creatures displaying magical abilities should be the stuff of myth and legend that's only recently becoming more understood and cataloged. Seeing an actual rare pokemon should be a once in a lifetime event for most people before the advent of pokemon capture, and even now mythicals and legendaries should only be acknowledged in-universe as singular existences that almost never came into direct contact with humans. Modern day pokemon that have self adapted to live near human civilization should be viewed as the foremost wonder of the modern age, along with the creation of Oak's pokedex