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Jhoto is a region that was populated for far longer than sinnoh and kanto, which means proper towns and world building can be made
Using the traditional japanese style to the maximum, we will learn about the creation of the pokemon league/gym system trough a few dojos
These "Dojos" are not actually monotype gyms, as they represent an idea or a school of thought, not a type. For example, the dojo of the creeping shadow, hidden deep into Ilex forest, will use a mix of dark, ghost, and poison types pokemon to use unconventional and "creepy" strategies, like perish song, trick room, etc.
The Dojo of the raging tempest (pic rel) might use both water and electric pokemons, it will be located in a town near lake ire (called lake of peace at the time, it is implied the lake will destroy the town one day earning it's name.
After beating all dojos, we will be challenged by the pokemon master, a hermit living on mount silver that is rumored to have never lost a battle.
Goldenrod doesn't exist yet, but Violet city and Ecruteak city do, with their famous landmarks being important centres of the community (now the burned tower is not burned and it's fully explorable)(maybe the player could see with his own eyes what caused the alleged lighting that burned it down as part of the plot)
Olivine city exists and it's the main way of the region to communicate with the outside world. It's the most modern one and doesn't have a dojo. It's where the main game starts with the player arriving there
Part 1