I don’t think that Kanto’s themes of urbanism vs environmentalism were poorly conveyed. Pokemon is partly based on the tension between older hobbies of bug collecting in the countryside against the more urbanized world of the 1990’s where children were spending less time in a natural environment. Kanto is built around an urban core of Saffron, Celadon, and Vermillion, which is off-limits at first. The player literally travels in a big loop that weaves around the core of Saffron City, traversing through natural cave systems and multiple built underground paths. The Pokemon of the most far-flung or rural parts of Kanto are the ones that most resemble wild animals from our world: Pidgey, Caterpie, Beedrill, Sandshrew, Ekans, etc. However, the core of the region is associated with fewer varieties of Pokemon. The ones that relate to pollution and urbanization, you mention Koffing and Grimer, notably are obtainable later in the game in a place that was destroyed due to a moment when science and technology being used to exploit Pokemon. There’s a contrast between Pikachu and Magnemite for where they’re encountered in the region initially, and lots more to be traced. Geography defining the Pokemon world isn’t new either: Hoenn is split up into geographic areas that can only be fully traversed by gaining the tools to cooperate with Pokemon in order to explore this overworld with techniques like Rock Smash and Surf. Hoenn is also about the divide between the land and the sea, but also how these coexist with each other. The region is shaped like a yin-yang symbol. Sinnoh is split by Mt Coronet, which bars the player from passing over the midline of the region twice before they’ve even got three badges.
Kanto’s themes of genetic engineering and the conflicts and harmonies between science and nature are present throughout the region. Pallet Town, Pewter City, and Cinnabar Island all have scientific institutions that are the defining features of their towns. Fossil Pokemon, Ditto, Eevee, Mewtwo, and Mew are deeply entangled with the tension between the natural world and the emerging ability of people to manipulate life. Yes, the Ditto and Mew connection is often a result of fandom over reading, but there’s an explicit theme that connects many of these Pokemon together just beyond the “all Pokemon are connected” theme. Whether or not there’s a direct connection between Ditto and Mew beyond linked locations and colors and Transform, let alone fanon trying to make it explicit, there’s a very unsubtle theme of genetics that many of these Pokemon are involved in.
These themes of environmentalism vs urbanization are why Team Rocket is villainous, as they exploit Pokemon in a world that is up front about how people and Pokemon become their best selves by coexisting and cooperating. It’s not coincidental that Team Rocket have presences in places like Mt Moon by stealing positive scientific discoveries, Pokemon Tower where they disrespect the lives of Pokemon, Celadon City being an urban hub and shopping district, and Saffron City and the takeover of a huge beneficent tech company. Team Rocket are less concentrated in the periphery, where they are outsiders. However, the urban core is their home turf, and their presence being a gate towards the end-game is pretty explicit in the theme of proving that cooperation with Pokemon trumps exploitation of Pokemon. The gifted Lapras even relates to this theme by being an endangered Pokemon and one that is entrusted to someone who demonstrates their commitment to cooperation. When Team Rocket is defeated, they’re basically exiled to the periphery. In fact, Johto does the reverse of Kanto during Team Rocket’s revival, having them begin causing trouble in the periphery before they finally convene and take over the urbanized core again, this time in Goldenrod City.
There’s much more to the games than you and others in this thread are recognizing. These themes are persistent throughout the series and are expanded upon further each time the world becomes larger. Johto is explicitly in contrast to Kanto with its ruralism, isolation, budding scientific institutions, traditionalism, and mysticism. This is hammered home even harder in the post-game exploration of an even more urbanized Kanto. The environmentalist themes never go away either. The villainous teams in the early part of the series explicitly use or sabotage technology and scientific discoveries, tying back to these themes of environmentalism and respect for nature: Team Rocket uses Slowpoke tails for money, broadcasts radio waves to force evolution, powers the Rocket Hideout with Electrode, and takes over the radio tower as a way to intimidate, propagandize, and revive. Team Magma/Aqua steal submarines and research and attack scientists, and Galactic do the same with the Valley Windworks (notably renewable energy) and Professor Rowan. There isn’t an organization in Pokemon that is saying nothing, and Pokemon is absolutely not “cowardly”
Bakugames. The evil organization of Alola existing on an artificial WHITE island called a “paradise” separate from the four islands of the region could not be less subtle. The invasive species motifs of Ultra Beasts and the associations between all of them and human encroachment on the natural world is trying to say something about the effect people in the real world are having on the environment, especially of the land that Alola is based on.
There are inevitably things about the world of Pokemon that fundamentally do not make sense politically or are just not coherent, and that’s okay. Pokemon is fantasy (like explicitly based on genre fantasy RPGs) and it’s not going to be a perfect reflection of reality. However, the games are trying to say more than they’re often understood as saying. There’s a justifiable amount of cynicism surrounding aspects like the dual-versions and trade evolutions that absolutely do facilitate the financial aspects of the series. However, the themes of connection and self-betterment in the series come out through these elements: you can’t become your best self without interacting with others and making connections.
These connections are also why I think the moaning about esoteric game design in Pokemon is shallow and misses the point. The paratext of the games is part of the experience of Pokemon as a social game: you won’t be able to catch every Pokemon or find every Pokemon without cooperating and sharing information with others. We attain mastery by making connections and cooperating with others. Older adventure games like original The Legend of Zelda are designed around players sharing information with each other, taking notes, using all of their resources, and cooperating to figure out the games. Pokemon isn’t any different, and it’s always promoted socializing with others to solve problems in the games. Trading, exchanging strategies, and sharing information about where to find Pokemon have always been core aspects of the series for this reason. The incompleteness of the two versions isn’t just to sell but also to drive people to interact so they can create more understanding and enjoy something together.
