Maybe we're all missing the obvious question, here:
Has anyone in the pokemon world ever TRIED to throw a pokeball at a person? Perhaps Ghestis could have been stopped by tossing an Ultra Ball at him...
On a serious note, I get what some people are saying, when you boil things down, its a bit strange. The environment- really the entire planet- revolves around the function of Pokemon and their interaction with everything. The entire world runs due to various pokemon, so where DO humans fit in?
The same could technically be said about our planet as well, though. The planet functions properly because of all the animal interactions that keep things moving; like bees and their pollination of flowers or trees and their removal of CO2 to produce O2 allowing life to thrive. Humans, once again, don't actually contribute to anything (other than reducing whatever damage they cause to the environment). It could be argued that this world wasn't really designed to accommodate humans either (or that humans don't have proper synergy with the planet like other species do).
I feel like I might have gone in circles a bit; am I making sense? Basically, I'm saying that ours is similar; humans are seemingly the odd-man out when the environment functions as it does because of animals and not us (if anything, we tend to make things more difficult). So to have the pokeworld be the same; revolving around them, it's not that crazy that humans dont seem to fit in there, either. Of course, there's always the crazy theory that perhaps Humans evolved from pokemon like Oranguru & Passimian in prehistoric times. Or, they themselves were the very first Hyperspatial pokemon beyond capture and have long since forgotten their true heritage!