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So I'm curious: I just thought of something while I was trying to think of ways the story could have been improved.
For those of you out there who think the whole concept of Dark Matter is stupid, let me pose this question for you: what if it was actually a Primal Mew?
Okay, so. Replace all of the Void Shadows in the voidlands with illusion Pokemon, sort of like during the one boss battle. Alternatively remove the Void Shadows entirely, and replace them with Pokemon who, in their sorrow and negativity at being turned to stone, basically went feral and wild.
Then, for Dark Matter itself, given we learn after the voidlands that it was fought in the past by Mew and a human, why not replace the generic fantasy RPG design with a Primal Mew? It would serve the plot twist of it being a part of Mew well, it'd feel more consistent with Pokemon since it wouldn't be a non-Pokemon, and it'd provide both a reveal and exposition at the same time, connecting it to Mew/the Partner having to accept it.