i have an idea on how to resolve the Yungoos and Gumshoos thing. What if there would be like a place in area where you could trade Yugooses and Gumshooses you caught for money or useful items or something? You would be told that the Pokémon are transported in their Pokéballs to their native region and released to wild, thus, in the long run, hopefully getting them all back where they belong. It’s just an idea though.
I kinda like this idea. It does run into the slight difficulty of drawing more attention to Yungoos’ home region, which doesn’t exist yet, but otherwise, it presents a significantly more sane approach to an invasive pest that’s still compatible with Pokémon’s baseline ethical framework.