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Make it a distortion world style dungeon, but thats obvious
Also, maybe make it like the Hoopa Rings in ORAS, but in reverse, where we travel to the find all the legendary pokemon instead of them coming to us,
Like maybe once we go inside, and it drops us off in Cerulean Cave where we can battle Mewtwo
If they dont want to recreate every single area for each legend, maybe just make it like a Legendary hub world or something