I think the latter parts of the story are incredibly cheesy, especially if you look deeply into it. Like, hate and jealousy are survival instincts yet these big bad evil thing, Dark Matter, can cause the world to end because Pokemon hate each other? I also hate Dark Matter's dialogue; every single time it speaks it sounds like a petulant child. Also, it seems like Dark-type Pokemon are screwed, because it manifests on darkness, so yeah, it's kinda stupid when there already is Pokemon who's entire existence is being dark.
We'd be here all day if I were to touch on how drawing the planet to the sun because the planet stopped spinning, because it's extremely ridiculous, even with creative liberties, in my own humble opinion. I don't believe a dime how the Tree of Life can keep a planet rotating, and besides, see what an axial tilt does to the climate of the planet...like summer? Imagine actually drawing it to the sun. Anyway, that's my personal problem and if anyone else is ok with it, that's totally cool.
Some of the twists seem kinda outta nowhere and I know the story does its best to explain, but they still feel like Shyamalyan twists. Near the end of the game, your partner is supposed to be a Mew incarnate, something that wasn't foreshadowed at the beginnings of the game. It felt like they just wanted a twist for the sake of it, and all of the explanation near the end just felt like a handwave. Also, Nuzleaf and Beeyehmen twist also seem a bit forced as well, but I would say it's less out of nowhere than the Mew thing.
Otherwise, the story is ok. I think I liked the beginning parts and the parts with the Expedition Society more than the parts near the climax, because the writing there is far too "srs business with Dark Matter who speaks like a 6 year old child" for me to actually take seriously.