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Plenty of things went right for a first game, but as the series has evolved, Kanto has become increasingly stagnated. If we ever do return there it should be with a massive facelift. Pic related. I based the design more closely on the actual Kanto region and divided it into prefectures. I tried to align each settlement, route and dungeon on the actual locations of their inspiration where possible.
SW (based on Shizuoka and Yamanashi, which amusingly aren't even in IRL Kanto)
>A - Pallet Town (Shimoda)
>B - Viridian City (Hakone)
>C - Indigo Plateau (Kofu)
>P - Viridian Forest (Chichibu National Park)
>Z - Victory Road
>! - Mt. Silver (Mt. Fuji)
NW (based on Nagano and Gunma)
>D - Pewter City (Maebashi)
>E - Alabaster City (new, Nagano City)
>Q - Pewter Quarry (Kusatsu)
NE (based on Tochigi and Ibaraki)
>F - Ochre Town (new, Utsunomiya)
>G - Cerulean City (Tsuchiura)
>H - Cobalt Town (new, Mito)
>R - Mt. Moon (Mt. Akagi)
>S - Cerulean Cave (Mt. Tsukaba)
>T - Power Plant
>U - Rock Tunnel
SE (based on Chiba)
>I - Lavender Town (Narita)
>J - Vermilion City (Chiba - allegedly Yokohama but lol geography)
>K - Fuschia City (Tateyama)
>V - Safari Zone
Central (based on Tokyo, Saitama and Kanagawa)
>L - Saffron City (Tokyo City)
>M - Celadon City (Saitama City - allegedly Shibuya)
>N - Amaranth City (new, Yokohama)
>O - Cinnabar Island (Oshima)
>W - Diglett Tunnel
>X - Seafoam Islands
>Y - Cinnabar Volcano
I've provided dotted lines connecting things for illustrative purposes, but try to imagine something a little more open world than just straight paths from A to B. Could probably afford to throw a few more dungeons in too.