Ok, hear me out.
Humans are weak as hell. Compared to Pokemon, they’ve got no semblance of a chance in a fair, one-on-one fight. Pokemon can breathe fire, or control nature, or shift the earth with merely a thought. Humans? We can... punch, I guess. Kick. And it’s far weaker than any fighting type.
When humans evolved in a world of Pokemon, they needed to find other ways to even the odds. Tools, first. Then makeshift weapons. Then machines. Civilizations sprung up out of necessity, specifically in places where humans could have a chance of surviving: breeding grounds. Fertile areas, full of resources, food, and great places to nest made these little areas less prone to extremely strong Pokemon, places like the Indigo Regions, or Hoenn, Unova, Kalos, etc etc.
And that’s probably it. These little places on the coasts of great continents, carved out of the wilderness with back-breaking effort and so so much time are the only bastions humanity has against the terrifying, powerful depths of whatever lies outside the borders. Crossing the wilds is unthinkable, it’s suicide. The only option for travelling between regions is by sea, or by air (excluding Kanto-Johto). So these regions are all that humanity has. Little islands of safety in a world of unimaginable power and strength.
TL;DR: Humans are survivors, and had to MAKE their place in the Pokemon World, because otherwise they would have gone extinct a LONG time ago.