I think at the beginning the creators of pokemon were not sure if they wanted their world inhabited by regular animals or not .But they have understood that a situation is rising here.
I believe, they don't want normal animals in their world and they are gradually working on it. See, we had more mentions of normal animals in the previous gens. than in the recent
ones.
So, I think it's the general idea that the pokemons mainly eat berries and fruits(that is to say, they are mainly vegeterians) and some like Aggorns and Sableye live on natural objects like rocks and metals.( Come on, Aggorn eats metal, does not neccesarily have to mean that it is eating aarons for dinner!)
Well maybe sometimes some pokemons do eat other pokemons for a better diet; but we shall leave that out of our imagination to avoid complexity.