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because they made Kanto the post-game. and as pointed out by above, there aren't any filler towns in Johto after Cherrygrove. ultimately if you try to incorporate more story it'd likely end up like BW where there is just an onslaught of story event after story event, many of them essentially...

tbh i'd say the reason why the story in Pokemon is so bland is largely because the regions aren't big enough to accommodate the size and depth of story that players want without having to backtrack a lot.

Gen I has Oak asking you to complete the Pokedex (because why not), Gen II has Elm asking you to deliver the egg and then you sort of secondarily are encouraged to take on the gym challenge, Gen III has you wanting to face your father and also go on an adventure, Gen IV has Rowan asking you to...

i honestly think the main issue is that the regions in their entirety (routes, cities, caves, forests, and all) aren't big enough to accommodate as big and deep of a story that players want.

short version: player choice is an illusion that typically masks terrible story-writing. freedom in the overworld would be a much better choice, though probably not applicable to Pokemon all that much.