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The item list's amazing too. The dummied out "surfboard" was Lapras, which was an item, and the whole Pokémon Tower, Fuji included, apparently played a more prominent role in the plot, since there's also a "Fuji Letter" in the items.
The weird sprite that appears in the overworld spritesheet seems to be pretty much confirmed for a monster icon. The "New Game Design" book cover might use a more complete version of that spritesheet, featuring the rest of the monster icons (plants, seals and such)