>>57825137Exactly, many of those decisions were made by the small number of Pokémon. The anime director admits that many of them were mistakes due to a lack of communication between the creative teams, such as a real horse in a movie before the creation of Muddsdale.
Now we have so many Pokémon that we can finally complete food chains and all kinds of interactions, leaving more specific things to ambiguous things like whether Pokerus or a wizard(Legendary) did it.
It's not perfect, but it's fun to see the worldbuilding of this world.