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The Ultimate Weapon in X and Y should have been where the Eiffel Tower was instead of a Gym. This makes more sense because Lumiose is in the middle of the region so is at a more strategic place for the Weapon to hit anywhere it wants. It would also explain WHY Lumiose City exists, because they built it slowly over time around the Ultimate Weapon (tho no one knew what it truly was besides AZ).
Also, instead of the route below Geosenge with all the graves of the Pokémon who died from the Weapon, you could instead have a spooky-ass section of the game beneath Lumiose called the Lumiose Catacombs, based on the Paris catacombs.
