Finally something that puts into words the vibes I get from this:

I think at some point between Pokemon Arceus and the games set in modern time, Pokemon and humans were viewed as equal and lived together, even marrying.
And with the Pokedex being a relatively new piece of technology and practice in Red and Blue, it's probably safe to assume that the Pokemon War Surge fought in might have had something to do with widening the divide between humans and Pokemon.