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A 4-star system that determines advanced enemy types and bosses. 1-star Pokemon are your typical Pokemon that your every day trainer will have. Pokemon rated 2 to 4 stars get buffs depending on their star rating- like the totem mons. However, the star rating determines how many Pokemon you can use against that Pokemon.
So a 2-starred mon will have a boost to its stats, maybe some other unique attributes, like typical JRPG bosses. But you get to use two Pokemon against it. A 4-starred mon has an insane boost to its stats and attributes, but you get to use 4 Pokemon against it.
Could be interesting to extend this to the player, too. Want to use a 4-star mon? Well have fun battling four Pokemon every battle. And you can mix and match, too. Against a 3-star mon you can use either a 2-star or a 1-star or three 1-stars.
Make the final boss the only 6-star mon in the game and there ya go.
So, like dynamax raids in some way only not completely shit.
All that said, I dont think Pokemon needs to fundamentally change its formula just to be harder. I mean, the competitive scene proves the system can be plenty difficult. They need to fix their AI so that trainers actually switch more, while giving said trainers actually good teams. Maybe add some more tension to gyms by not letting you save inside them and booting you back to the beginning when you lose. Maybe drop the “gyms being in buildings in towns.” Make the rock gym deep in some cave or the water gym in the middle of the sea.