To be fair, Black Isle had already fucked up Fallout with the release of the second game.
FO2 had disjointed worldbuilding because writers were allowed to design their own areas without any coordination with others on the team, there were a shitload of cringe pop-culture references, and far more edgy bullshit than in FO1, plus retconning the vaults into nonsensical experiments and part of a government conspiracy because the X-Files were popular back then.
Bethesda's sin is doubling down on the faults of FO2, instead of course correcting like New Vegas did, and not building on the positives.
FO3 is a combination of the worst aspects of FO1 and FO2.
I never understood this argument, there is only a couple of lines about the vaults in Fallout 2 and none of them really make the setting worse. You know what Fallout 2 also introduced? The Enclave, the experiments make perfect sense with them around pulling the strings, where as Fallout 1 that didn't have them stuck to the vaults being controlled and working as intended(even then, what about Vault 12? It's never confirmed if it's builders were just incompetent or the vault door not closing was part of the experiment, so even then what Fallout 2 did was hardly a retcon. Same goes for Vault 15, where the experiment was essentially multiculturalism and it ended up giving us some of the worst raider gangs in the setting plus NCR, which is arguably even worse depending on your outlook). You can either have Vault Tec be a generic corrupt company making crappy vaults that don't work or have them work with the Enclave in order to test out theoretical space travel scenarios to prepare humanity for leaving the Earth, the latter is infinitely more interesting and vast majority of vaults do indeed have something resembling tests that would benefit a voyage in space.
The vaults were actually one of the better parts of Fallout 3, both as dungeons and world building. The reason they're better in Fallout New Vegas is the same reason pretty much everything is better: good writing. Compare Vault 108 with Garys and Vault 34 with Boomers, both of which had pretty much the exact same experiment. Still, that's pretty much the only interesting vault in New Vegas alongside 22, unless you count 21 as well, where as Fallout 3 had Vault 101, 106, 87 and 92 which were all decent dungeons with interesting ideas. Compare that to Vault 19, where the only interesting part of it is the story, outside of that you're just killing bugs and other weak enemies in a crappy dungeon looking for holotapes(which ironically enough is your typical Fallout 76 experience). Also, I will disagree with you on F3 being the worst aspects of F1 and F2, as F3 barely followed the ethos of these games at all. What the game resembles more is Oblivion with a Fallout overhaul mod, which goes about how you would expect: it's Elder Scrolls with guns. Every single problem the game has is a Bethesda problem, a unique laundry list of faults not really seen before or since within the franchise. As time went on, they also got worse and worse, makes the forced pop culture references of Fallout 2 look quaint in comparison.
You forgot to mention that despite locations in Fallout 2 being wacky, they somehow all work within the setting, New Reno might look stupid in a vacuum but it is a major political player within New California, mentioned by many other NPCs and locations and so it feels like a real place that's somewhat grounded within the setting. We even got inter-politics going on, like NCR invasion of Vault City or New Reno flooding Redding with drugs, what does Fallout 3 have? How does Megaton interact with Rivet City or Underworld? What does Republic of Dave or Big Town bring into the bigger world? The answer is nothing because Bethesda designed Fallout 3 like they designed Oblivion, it's just a series of shitty little isolated villages that don't interact with one another, unlike the locations in Fallout 2 and even 1. Hell, even the locations don't make sense, dare I bring up the "what does Megaton eat?" question that the tourists and anime avatar cretins in this thread seem to hate for some reason(because they can't answer it)?
Nobody asks this about New Reno or any other Fallout 1 or 2 location because they were designed by real writers, not Emil, and so they feel real enough that even if we don't see Brahmin or crops on the map, we can fill in the blanks since there is something resembling a society in California, the towns can import what they need for exports of what they produce or don't need.
Meanwhile, the very first dungeon of Fallout 3 already presents a narrative problem we never get an answer to, a complete failure in storyworld building
Remember when people mocked Toxic Caves or Vault 15 in Fallout 2 and 1 because they didn't make sense? What's that, nobody did because they were well designed dungeons that NPCs actually talk about, as if they exist in the game world? There is zero mentions of Springvale School and what it brings to Megaton, despite the raiders there apparently being a problem for the town. What about Silver, the first NPC you are likely to encounter outside of Megaton, what's her deal?
Remember when people mocked Shady Sands or Klamath for their NPCs not making any sense? What's that, nobody did because these locations were designed like real villages and simple questions like "what do they eat", "where do they live" and "where do they shit" were all answered? I think you get the point, these are all very much Bethesda problems, lore and worldbuilding are not one of the problems the older games had even at their very worst. That came later.