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Mr Khan said:

You'd figure Shikoku would be the obvious choice, since the last two represented Kyushu and Hokkaido

Shikoku would be too small alone. The regions in Pokemon are actually all scaled correctly for their size in the game. In other words, Kanto:Kanto is the same proportion as Sinnoh:Hokkaido. So Shikoku alone would be far too small.

@Son1x, Tohoku is about the right size, but far too geographically plain. It doesn't have enough interesting features to make for a good Pokemon game, and it's not set up to have much available in the way of water pokemon/ocean stuff, which is always important for a Pokemon game. It's also an awkward shape for the standard squarish Pokemon world map.