This is an excellent question, one that has plagued many pokémon researchers since the dawn of, well, pokémon research. What makes this question even more difficult to answer is that some pokémon clearly possess human-level sapience as well as intelligence, and there is absolutely support for the idea that pokémon would be perfectly capable of building their own civilizations if humans were to suddenly disappear one day.
The prevailing theory is that humans and pokémon form a symbiotic relationship in which pokémon rely on us far more than we on them. While wild pokémon can get stronger and develop their powers on their own, it’s far easier to do so by bonding with a human. This is supported by the fact that some modes of evolution—most notably those associated with trading—are far easier to achieve via human interference. It likewise falls in line with the Sinnohan story concerning the idea that once, long ago, humans and pokémon lived in harmony due to an agreement made among all pokémon to help humans in their development.
The other theory—which in my opinion is merely an extension of the above, but some thoughts within the scientific community differ on that point—is that the arrangement is by necessity. It’s a bit like asking why bears aren’t the dominant species, even though they are both intelligent and higher on the food chain than we are. Whereas animals and pokémon have both naturally adapted plenty of tools they would need to survive, humans have not. Instead, we’ve developed a sense of ingenuity: the ability to reason and create. That isn’t to say that pokémon aren’t capable of creating or reasoning; it’s more to say that this isn’t their primary mode of survival, as they rely much more on their powers. Whereas humans have built cities, learned to form global networks with one another, and created devices to harness the elements (both in the form of pokémon and in the form of the literal elements themselves), pokémon spend much of their time honing their own abilities and learning to defend comparatively smaller groups of their own kind and parcels of territory.
In short, there are very likely at least two possibilities. First, pokémon benefit the most from a symbiotic relationship with humans if the humans in question were allowed to flourish and develop. Second, we actually are just as advanced as pokémon, and it’s the ability to adapt and create that’s enabled us to maintain our place in this world.
(And a sobering third: pokémon simply allow us to be the ones in charge.)
The Pokédex According to Bill 