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National Park is shaped like a pokeball, Lake of Rage used to have a town in beta, and the daycare egg in GSC gives you a range of baby pokemon all having a 12.5% chance of being shiny or some crazy shit, I got a shiny magby once
Also GTS was planned as early as Crystal and some rooms and text for it can be seen in beta, but it was scrapped presumably due to memory issues and it not being fully developed yet