>>49161989The vision of the franchise became very, very different partway through Gen 2's development due to Pokemon's success and the cultural zeitgeist that was Pokemania, and even as early as GS they were trying to clean up the original plot points and implications that RGB set up.
No longer was the Pokemon world implied to be similar to the real world at its core but with a mysterious phenomenon (implied heavily to be radiation due to all the poison types and the existence of Grimer and Koffing) that caused these new creatures to appear and replace normal animals, but rather these creatures have almost always existed from the start and people haven't yet figured it out.
Then once RS came, the franchise started sorting its identity out and became a proper idealized fantasy world removed from ours where Pokemon are the only creatures other than humans, and any lingering details were gradually scrubbed out when possible (usually once they had a suitable idea for a replacement that better suits the current brand, as seen with the Mewtwo excerpts).