The Pokémon world has its own geography, but almost every Pokémon is based on a real animal, plant, or folk tradition. That means you can ask a fairly reasonable question: if these things existed, where on the actual planet would you find them? Not the Kanto region. The real Kanto, which is a plain in Japan. Or the Amazon, or the Australian outback, or the Scottish Highlands.
This is my attempt at that map. It is not canonical and it is not science. It is a thought exercise built on what the Pokémon are obviously modelled on, and a bit of geography. I have tried to keep it honest, which means a few of the obvious answers are wrong in interesting ways.
Japan gets the obvious ones
Most of the early roster is Japanese in origin, so this is the easy part. The Kanto games were set in a fictionalised version of the real Kantō region around Tokyo, so a huge chunk of Gen 1 is just local fauna drawn with extra steps.
Slowpoke is based on the giant salamander, which still lives in Japanese mountain streams, so Slowpoke and Slowbro belong in the rivers of Kyūshū and western Honshū. Shellder and Cloyster are bivalves, so any cold Japanese coast. Magikarp is carp, and carp are everywhere in East Asian rivers and rice paddies, so Magikarp is essentially the national fish of any lowland Japanese waterway. Gyarados is what happens when one of them gets angry, so the same rivers, just less of them.
Meowth is a cat, but the coin on its head is a maneki-neko reference, so it belongs outside Japanese shops and temples, which is exactly where it lives in the games. Chansey and Tauros are Safari Zone mons in Kanto, and the Safari Zone itself is modelled loosely on a nature reserve, so they stay in southern Japan in this map.
Voltorb and Electrode are the exceptions. They are Poké Balls that gained sentience, which means they do not have a habitat, they have a supply chain. They live wherever humans manufacture balls, which I would put near any industrial city.
Southeast Asia is the jungle roster
Anything based on a tropical rainforest species goes here. Bulbasaur is a toad with a plant on its back, and toads with unusual dorsal features live in tropical Asia, so the Bulbasaur line belongs in the lowland forests of Borneo or Sumatra. Tangela is a tangle of vines, and vines that dense are a rainforest thing, so same region, lower canopy.
Oddish and Bellsprout are both built on plants that thrive in humid, warm climates. Oddish looks like a radish that walks, and Bellsprout is a pitcher-plant derivative, so put them in the wetter parts of Indonesia and the Philippines. Vileplume is explicitly based on Rafflesia, the giant corpse-flower that actually grows in the rainforests of Sumatra and Borneo, so Vileplume has a real, pinpointable home. That one is not even speculation.
The monkeys, Aipom and Mankey, are New World and Old World monkeys respectively. Mankey is a pig-tailed macaque type, which lives across South and Southeast Asia, so Mankey belongs in the forests of India through to Vietnam. Aipom is a prehensile-tailed monkey, which is Amazonian, so I am moving Aipom to South America below.
Australia gets the weird mammals
Australia is the easiest case after Japan, because so many Pokémon are marsupials or monotremes that only exist there. Kangaskhan is a kangaroo with armour. It belongs in the Australian outback, full stop. The fact that it carries a joey in a pouch means there is no other candidate region.
Wooper and Quagsire are based on axolotls and mudpuppies, which are neotenic salamanders that keep their gills as adults. Axolotls are native to a single lake system in Mexico, so strictly the Wooper line is Mexican. But the vibe of a sluggish, smiling, water-dwelling mud creature fits the billabongs of eastern Australia well enough that I am giving Quagsire a second home there. Wooper stays in Mexico.
Numel and Camerupt are camels, so they belong in the arid belt that runs from North Africa through the Middle East into Central Asia. The Gobi and the Sahara are both fine. Slugma is a snail made of lava, so it lives on actual volcanic slopes, which puts it in Hawaii, Iceland, or anywhere along the Pacific Ring of Fire.
South America owns the river and the rainforest
The Amazon basin is the most biodiverse place on the planet, so it claims a lot of Pokémon by default. Anything based on a brightly coloured tropical bird, so Chatot, and anything based on a poison dart frog, so the Croagunk line, belongs here. Croagunk is specifically a dark-coloured frog with warning markings, which is dart-frog behaviour, so the Amazon tributaries are its home.
Piranha Pokemon are Carvanha and Sharpedo. They are literally named after piranhas, which live in the Amazon and Orinoco, so the Carvanha line is South American river fauna. Barboach and Whiscash are loaches and catfish, so they fit the slow, muddy rivers of the same continent.
Treecko is a gecko, and geckos are global, but the arboreal, forest-dwelling geckos with bright green colouration are most diverse in the Amazon and the Caribbean. So the Treecko line goes in the rainforest canopy. Breloom is a mushroom-lizard hybrid, and the idea of a toxic, spore-shooting reptile is a rainforest concept, so it stays with Treecko.
Africa gets the savannah and the megafauna
Africa is where the big grazing and hunting mammals live, so it claims the Pokémon that are clearly based on them. Girafarig is a giraffe, so the savannah belt from Kenya down through Tanzania. Its tail has a second head, which no real giraffe has, but the habitat is uncontested.
Pyroar and Litleo are lions, so they belong in the same east and southern African savannah. Zebstrika and Blitzle are zebras, so the same grasslands. Rapidash is a fire horse, and horses are domesticated, so Rapidash is less a wild animal and more a ranch animal, which I would put on the Eurasian steppe rather than Africa.
Hippopotas and Hippowdon are hippos, so sub-Saharan rivers and lakes. The real hippopotamus spends most of its day submerged in fresh water in Africa, and the Pokémon version does exactly the same thing, so this is the cleanest habitat match in the entire roster.
Donphan is an elephant, and Phanpy is a calf, so they belong anywhere elephants do, which is the African savannah and the South Asian forest. I lean Africa for Donphan because of the rolling, dusty terrain it is shown in.
The Arctic and sub-Arctic take the ice types
Anything with Ice typing that is based on a cold-climate animal goes north. Seel and Dewgong are seals, so the Arctic coastlines of Canada, Greenland, and Russia. Spheal, Sealeo, and Walrein are walruses, so the same region, specifically the pack ice.
Sneasel is a weasel, and weasels live across the northern hemisphere, but the snow-and-darkness theme puts it in the sub-Arctic, so northern Scandinavia and Siberia. Swinub and Piloswine are pigs, but they are based on musk oxen and mammoths, so the tundra. Mamoswine is a woolly mammoth, which means it is technically a ghost of the Pleistocene, but if it had a modern range it would be the mammoth steppe, which no longer exists, so the closest living equivalent is the Siberian tundra.
Avalugg is an iceberg, so it lives wherever icebergs calve, which is Greenland and Antarctica. Bergmite is a chunk of ice, so the same coastline.
Europe gets the domesticated and the folklore
Europe is where a lot of the folklore-based Pokémon belong, because the folklore is European. Houndoom is a hellhound, which is a medieval European church motif, so the dark forests of central Europe. Absol is based on the western idea of a disaster omen, which has no single real species, but the white, mountain-dwelling body type fits the Alps, so Absol lives on alpine peaks.
Murkrow is a crow, and crows are global, but the witchcraft association is European, so Murkrow belongs in the British Isles and central Europe, in the same woods the folklore came from. Misdreavus is a banshee, which is Irish and Scottish, so the western Highlands and Ireland.
Growlithe and Arcanine are dogs, but they are modelled on the Fu Dog, which is Chinese, so I am actually moving them to East Asia. Growlithe is a Shisa, the guardian lion-dog of Okinawa and southern China. So despite the European name in English, the origin is Chinese and Ryukyuan.
Ponyta and Rapidash are horses, and the wild horse, Przewalski's horse, lives on the Mongolian steppe. So Ponyta belongs on the Eurasian steppe, which is also where Rapidash belongs if you want it wild rather than domesticated.
North America gets the bears and the birds
Ursaring and Teddiursa are bears, and the brown bear that matches their build lives across North America and northern Eurasia, so the Rocky Mountains, Alaska, and the Siberian taiga are all fair. I lean North America for the sheer scale of the wilderness, which fits Ursaring better.
Pidgey and Pidgeotto are pigeons and hawks. Pigeons are global, but the rock dove, which is the ancestor of the city pigeon, is native to European and North African cliffs. So Pidgey in the wild belongs on Mediterranean sea cliffs. In a city, Pidgey belongs everywhere, because feral pigeons are everywhere.
Fearow is a raptor, and raptors are global, but the long, pointed-wing build fits the falcons, which are most diverse in open country. So Fearow belongs on the Great Plains or the Eurasian steppe, anywhere with big skies and small mammals.
Braviary is a bald eagle, which is North American, so Braviary is unambiguously Canadian and American. Mandibuzz is a vulture, and vultures are most associated with the Americas and Africa, so the condor range of the Andes and the American Southwest works.
The ocean is its own region
A lot of Pokémon do not belong to any country because they belong to the sea. Tentacool and Tentacruel are jellyfish, which are global, so any warm ocean. Relicanth is a coelacanth, which lives in deep water off the coast of East Africa and Indonesia, so Relicanth has a real and very narrow range.
Wailord is a whale, so the open ocean, specifically the cold, nutrient-rich currents where baleen whales feed. Kyogre is a myth, but the myth it is based on, the Leviathan, is Levantine, so if it had a home it would be the eastern Mediterranean. That is a stretch, but the whole category is.
Lapras is a plesiosaur, which is extinct, but the closest living analogue is the leatherback turtle, which travels whole oceans, so Lapras belongs on migratory sea routes. Sharpedo is a shark, so tropical and temperate coasts worldwide.
Where the legends would live
The legendaries are the hardest because they are ideas, not animals. Zapdos is a thunderbird, which is a North American Indigenous spirit, so Zapdos belongs over the Great Plains and the Rocky Mountains. Moltres is a phoenix, which is a Eurasian and Middle Eastern motif, so the volcanoes of the Mediterranean and Anatolia.
Articuno is a cold-weather bird spirit, so the Arctic. Lugia is based on the Ryūjin dragon of Okinawan and Japanese myth, so the seas around the Ryukyu Islands. Ho-Oh is the Chinese fenghuang, so it belongs in China, despite being the mascot of a game set in a fictionalised Japan.
Rayquaza is a sky dragon, and the sky dragon myth is East Asian, so the same region. Kyogre and Groudon are the Leviathan and Behemoth, which are Near Eastern, so the Red Sea and the eastern Mediterranean are the closest real anchors.
The honest version
The real answer is that most Pokémon are hybrids of a real species and a concept, and the concept is often Japanese, so the honest map is messier than the one above. Vileplume is Sumatran. Growlithe is Chinese. Houndoom is Bavarian. Braviary is American. The same game reaches across five continents for its inspiration, which is a big part of why the world feels so dense.
If you want to test how well you know the origins of these things, the Pokédex Trivia game will hand you an entry with the name blanked out and ask you to guess. The habitat tells are often the giveaway, because a lot of the descriptions are quietly describing a real animal in a real place, just with extra powers attached.