Could it be that the population was denser as befitting the closeness of their cities, but that their numbers have dropped recently? We were taken from our worlds and brought here; the opposite could also have happened.

The ability to poison regular animals or set them on fire would give Pokémon an undeniable advantage, but that means little. My world has both powerful magical monsters and normal animals, and all thrive easily enough. Then again, as their habits and roles are not the same, they are less likely to compete in the first place.