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I’ll touch on something I haven’t read someone post yet. Hoenn is designed with balance and harmony in mind.
The region is split between Pokémon and humans in a very unique way that isn’t really replicated in other games. Think to the first forest-like routes and towns that gradually open up to a seaside metropolis.
Rustboro is not a defiance of nature however, but exists due to the less green parts like rocks and minerals. Devon started by selling iron and rock, and now they supply all kinds of products and even revive fossils. They were carving out a tunnel, but stopped so as not to disturb the local wildlife.
The cycling road really shows the whole theme of Hoenn very explicitly through a piece of dialogue from an old man. He says something along the lines of “one path above for humans, one path below for Pokémon. Separate but equal, maybe that’s how it should be”
The cycling road is a demonstration of coexistence between the people and monsters by leaving nature intact instead of destroying it.
The residents of Hoenn are very connected to the areas they inhabit, and this is evidenced both by dialogue and activities. The ash ridden route 113 and Fallarbor have carved out a life in the shadow of Mt. Chimney just like Fortree City has sprung up from nature itself and fused with it to compose one of the most atmospheric set of routes and areas in any Pokémon game in my opinion.
The plot also emphasizes why you shouldn’t throw off the balance of nature. It is pretty on the nose, but it’s the centerpiece of the theme after all.