my theory is simlair to Iveechan's except that rather then the pokemon world being just an archipelago, it's an entire planet. All the landmasses are shaped like the islands of Japan, only on a much larger scale, about as big as continents.
So where did the Humans come from?
from Space, the humans originally came from space.
In the planet's distant past, visitors from another planet came to the current one for an unknown reason. They set up a colony on the planet and brought their technology with it, the visitors was at very cruel, to the native creatures, the pokemon, who lived in peaceful harmony on the planet before they came, and even to their own kind, as they constantly did genetic experiments on themselves as well as pokemon.
then for some unknown reason. The visitors were abandoned, probably by their homeworld. With it, almost all of their advanced technology was lost, especially space travel. The only bits and pieces their once very advanced technology survived, such as pokeball technology and matter transportation. With the help of ancient pokemon, the visitors took up residence in the pokemon world.
Eons passed, The decsendents of the space vistors now live in a the world full of strange creatures, with technology they don't even understand completely, information with no known origin, and no idea about their true origin...