I've always had to restrain myself on pointing out that boning some Pokemon is infinitely less problematic that raising them to fight. Alakazam is smarter than its trainer as a general rule and a lot of these ghost types and legendaries are just people.

Ultimately I just don't think very hard on these things when playing my overpriced pet simulator. And I still think the Poke Pelago is way less messed up than the solitary confinement of a Pokeball, but again, I digress.