Team Nebula. Hyper competent mystery school occultists who actually manage to win in the events of the intro, interrupting the "Welcome to the world of Pokemon, people call me the Pokemon Professor" speech. Their boss utilizes an ancient Arceus expy to obliterate and reset the multiverse... Leaving only the old universe's professor, a single grunt, and himself surviving in the new world. The three part ways, leaving the player to encounter the betrayed grunt who wants to rebuild Team Nebula and rule with an iron fist, the boss who wants to find the legendary Pokemon to reboot the universe again because this new one is still too reliant on relationships (between people, between people and Pokemon, etc), and the professor who wants to stop them both. Aesthetic of spooky robes and iron half masks, carrying a candle. They'd use Chandelure line and other spookymons.
As an added bonus, small time crime syndicate Team Chance runs various rackets and think the legendary pokemon would be a good way to create infinite money out of nothing, and get in way over their heads. They'd dress like Vegas high rollers and use things like Krookodile and probably some new dice Pokemon.
After beating Team Nebula into the dirt, catching the legendary and box monster, becoming champion, Team Chance manages to steal all of the player's Pokemon, and the postgame involves fighting them with the old universe professor's Pokemon and building a new B Team, eventually fighting your hall of fame team, and being the very best, like no one ever was.
