Unpopular opinion, Fallout 3 and 4 are both Post-Post-Apocalypse in their own ways and haven't strayed from the initial concept of the Fallout series.
The reason this may be hard for most to see is the games take place with either wars in progress or in places on the brink of war. Fallout 3 has your character come out to a wasteland where the war between the Super Mutants and the BoS has been going on for some time and the threat of the Enclave is then added onto THAT. Civilization obviously will take some pretty big hits when a location goes from severe radiation, to new monsters (Things like Deathclaws), to war, and then to another war. And yes, that can even stretch out over a couple hundred years. The apocalypse was the radiation and the monsters, the post-apocalypse was establishing trade routes and settling cities, and the post-post-apocalypse is the wars that are breaking out after most people have settled down and reestablished trade. Raiders existing makes sense as well since bandits and such historically frequently come from remnants of armies or towns ravaged by war. So you have a civilized location plagued by bandits and nonstop war. Still post-post-apocalypse. These same things can be seen in New Vegas, the shining example of what people want in the series
Fallout 4 is even closer to the New Vegas's tone as much as a lot of people probably hate to hear that. It's an area where the whole thing essentially recovered aside from a few locations that are still plagued by irradiated creatures or Super Mutants. There are farms dotting the landscape with a few small towns and one or two major cities. The biggest difference is the Commonwealth is dealing with the Institute and hasn't progressed as far so the towns and cities aren't as large.
While each setting clearly has it's own level of progression, that doesn't stop the games from all being post-post-apocalypse as civilizations historically don't have a set amount of time before they get to certain stages since any number of things can happen to hurt progress. And one of the biggest things that can hurt or even aid progress is war, and "war never changes" IS the main theme of the series.
Any differences in tone come from the difference in each location's setting and shouldn't be looked at as Bethesda straying from what made the games great but instead a realistic approach to civilization.
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