The fact that, in the world of Pokemon, humans are still the dominant species. In our world, we only managed to become supreme because of our intelligence, and the technology it produced. In the world of Pokemon, there are Pokemon like Slowking, Alakazam or Metagross. They are more intelligent than humans, and far stronger. Why are these Pokemon not ruling the world instead of humans?
And that is a really good question that I have devoted much thought to. If we want to assume that Darwinian evolution and natural selection are still factors in the Pokemon World (which we can assume they are, as Mew is the common ancestor of all terrestrial Pokemon), that leaves two options available for the existence of humans. Either humans evolved the same way there as they did here, meaning from normal animals. This would, of course, require that normal animals exist in World of Pokemon. While the early anime and some Pokedex descriptions to contain obscure references to real-world animals, I personally classify these as non-canon instances of fourth wall breaking. If normal animals existed, we would be seeing a whole lot more of them. The second possibility is that humans evolved from Pokemon. I see this as the likely scenario. If that is the case, that means at some point in history, evolutionary pressures caused humans to lose the abilities that would classify them as Pokemon. One thing to point out is that humans may not be the strongest, or even the smartest, but they do have one advantage over every Pokemon. They can use technology. It doesn't matter if an Alakazam is as smart as a supercomputer, it could never build one. It's a similar scenario to the dolphin. Some suggest that the dolphin is intelligent enough to build its own civilization. The only thing that holds it back is the fact that it is nearly impossible to create the necessary tools in an underwater environment. So I suggest that early in evolutionary history of the Pokemon World, the first proto-humans focused on the use of tools rather than the use of powers, leading to the hierarchy of Pokemon and humans seen today.
To draw upon another one of my theories (this one about the morality of Pokemon training), it is also possible that Pokemon, being the natural born battlers they are, respect the human ability to come up with strategy and plan ahead so much that they evolved to work with humans instead of against them, allowing humans to survive and become dominant.
