This is my theory on Hisui's backstory:
In the beginning, there actually was an ancient civilization that had a relationship with Pokemon. The civilization's relations, however, were not that beneficial for the Pokemon. Instead of befriending Pokemon like the anime encourages, the ancients developed (or adopted) the PokeBall solely to catch and enslave Pokemon.
Sometime later, Arceus discovers that humanity was mistreating Pokemon and decided to transfer some of its power to several of beleaguered Pokemon. In exchange for that power, however, they went insane and tore apart many of the cities within the civilization, reducing it to villages like Jubilife. To convince the remaining villagers to lead separate lives from Pokemon, it left these corrupted Pokemon as they were.
Only a handful of brave souls, such as the Galactic Research team, have the courage to reconnect with Pokemon. Therefore, as the main character, your goal is to make up with Arceus to stop the corrupted Pokemon and establish modern-day relations between people and Pokemon.