See this? This is a map of what Kanto used to look like. It's a bit out of date. We've made the changes we could, but no one's really able to perform a cartographic survey these days.
On a purely physical scale, we've found a few major changes. Cycling Road was destroyed, though you can still see chunks of it sticking out of the water. The Indigo Plateau is now the Indigo Sea. And Cinnabar Island, unlike the one you encountered in the games, actually does look like it does on this map – it's just a volcano now, no people live there or anything.
What is going on these days, then? Though we haven't produced a map, here at the Pewter Museum we have contacts throughout Kanto, so we've been able to get a decent handle on what's going on in the major cities: monitoring all the shifting little fiefdoms, on the other hand, is pretty much impossible.
(That said, if your character is playing as ruler of one of those shifting little fiefdoms, send me a message and I'll PM you a map of your general region.)
Pallet Town is an oasis in the desert of apocalypse, a small hamlet which functions more or less as it did before the nuclear war. This is typically ascribed to the leadership of Professor Oak, an eccentric, half-mad researcher who sends children out into the world with Charmander, Squirtle, and Bulbasaur as though the war never even happened... and who has one of the most powerful pokemon collections in the world. Some say he could bring order to Kanto again and get the survivors back on their feet, but he just doesn't care enough.
Viridian City didn't get nuked, because Team Rocket's American branch knows how to place a bribe. It did, however, get besieged soon after, and its sack at the hands of Rocket victims was arguably worse than a nuclear bomb. Most of its buildings are leveled and the city as a whole is divided between various individuals who claim to be the rightful successors of Team Rocket's legacy.
Pewter City is under the benevolent rule of the Pewter Museum, which is in no way a front for the mad museum head who sees this as his opportunity to reverse the various mass extinctions in pokemon history and bring back the age of Kabutops, Omastar, Aerodactyl, and others.
Cerulean City is a republic out of the finest traditions of Renaissance Italy, with power vacilitating between noble and merchant houses and peasants every election, war, or coup d'etat. It's more or less unified, except for the family compounds – wars happen quickly there. Most recently it was controlled by a bicycle gang hired by the bike shop owner, one of the richest men in the town.
Lavender Town is a theocracy under the leadership of the Temple of Arceus, one of the larger post-apocalyptic religious sects – there are many similarly named ones (Church of Arceus, Shrine of Arceus, etc.) which dot the landscape in various small villages. The leader lives a humble lifestyle and both humans and ghost pokemon follow him with fanatical zeal – indeed, he is seen as a leader of the faith by an increasing number of acolytes around Kanto.
Saffron City is a communist dictatorship formed when the workers rose up against the President of Silph Corporation. Whatever your opinions of communism, this particular communist state is a brutal dictatorship. They wage fanatical wars to export a revolution while working the people as hard and for as little pay as Silph worked them, offering only the promise of a better tomorrow. They have attracted many people outside of Saffron with nice talk of a better future and a war against the gods.
Saffron is frequently at war with Celadon City, and Route 16 (which connects the two) is believed to be the only one in all Kanto not dotted with fiefdoms and brigands, because the two largest cities find it too important an invasion route. This is because Celadon City is something of a company town, dominated by a consortium of local businesses led by the Celadon Department Store. Erika, uniquely among the Gym Leaders, is actually a popular figure in the city and rules its walled southeastern quarter. She is seen as leader of the opposition and was once leader of the Pokemon League's remnants, but has since relinquished this title to Lt. Surge.
Vermilion City is a bustling port which has seen an economic boom from the renewed importance of sea communications: it has regained half of its prewar population. The southern half of the city is ruled by Lt. Surge, while the northern half is ruled by a warlord named Earnwald who specializes in flying pokemon. One of the more interesting organizations within is the Pokemon Fan Club, a group which keeps pokemon as pets, enters them into contests, and defends its compound not with pokemon, but with guns.
I frankly do not know what is going on in Fuchsia City, for it is on the other side of Kanto, and they say whoever rules it has adopted a policy of isolationism and does not even want information to get out. They will, however, trade, and great wealth can be found if you are prepared to make the journey... and have something of value to offer.
Thank you for visiting the Pewter Museum. I hope you found our information to be of use.