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This games whole fakeout and babby SMT thing it has going on honestly might have become one of my favorite plots in a Pokemon game. I love the idea of being the first trainer, and bringing Pokemon and Humans together into the symbiotic society we all know and love from the series. And the idea of seeing characters ancestries and shit is cool. It certainly helps that the story was presented with something resembling respect, so instead of "DUDE WOWWEE ZOWEEE ISNT ISLAND LIFE COZY" you get "You can help us, or, yknow, die in the woods for real", the curt disapproval Cogita has for Volo feels like something that couldn't have existed in another Pokemon game.
My single complaint with the story really is in how the time period is presented. Some characters wear period appropriate clothing. But then you have diamond clan members in yoga pants, beanies, and hoodies a lot of the time. Which is especially odd considering you the player don't even get access to pseudo modern clothes like that, so it was hardly a measure taken in case of players not jiving with the past setting.