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I believe the only way to do a "Pokemon killer" that is taken seriously is not to reference Pokemon, but to reference the experience of playing Pokemon for the first time.
So instead of a happy-cheery world, make it about a bunch of kids who have a monster-catching interest that the world doesn't really care about. Take a page out of Dark Souls and make everything slightly too big to sell the feeling that you're playing as a kid. Have the player explore backalleys, abandoned buildings and closed passageways, something all kids want to do. The goal is not to make the player feel like they're playing a Pokemon game, but like they're a "kid interested in Pokemon" again.