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I swear every complaint about UBS are from people that don't play video games other than pokemom and because of that can't see how super bosses would add to the game in format, especially with the totem system. If the UBS turn out to be aliens or creatures the future foundation made that need to be stopped, thematically it would make the world deeper and when you fight them make the game feel more akin to the anime or manga, you have your small team take down a giant like UB2? Kids would love it, you'd feel closer to them and the world.
From a gameplay standpoint they could come up with beefed up stats, custom moves and maybe do a play on the totem system where they'd summon lesser ultra beasts or other ultra beasts. This would be challenging yet fun like a legendary fight.