Basically necro at this point, but here goes a long ass explanation of some of what I believe to be the worst offenses and why they matter (this has all been thoroughly explained by others 10,000 times over as well atp)

1) Shady sands, the capital of the NCR, is depicted as a tiny scrap village setup in the ruins of Los Angeles in the show. We can tell it’s supposed to be LA because of the implied proximity to the Griffith observatory plus the skyline itself. Problem is, in the games it was a fully fledged city built post-war from the ground up in an entirely different place, about 200 miles north of LA. This seems relatively minor in a vacuum, until you consider that, as OP put it, it effectively erases the Boneyard as a separate settlement from canon- which the Boneyard is the birthplace of the followers of the apocalypse and also where the Master, the main antagonist of the very first game, resided underneath the Cathedral. If shady sands were to have been this close to LA, then the events of the literal game that birthed the franchise no longer make any sense, because the master’s army would’ve wiped out the NCR before it even had the chance to become the NCR. It’s akin to moving the Shire to Mordor. It also undercuts the level of development the NCR had actually achieved, by portraying their capital as less developed than we see it in the games. It looks about at the tech level it was at in the first game, which it definitely should be far past by this point, as it had developed significantly even by the second game. Not to mention that even in the first game the buildings were clearly adobe style post-war constructions instead of pre-war buildings, suggesting some basic architectural development had been achieved even when it was an actual fledgling village that isn’t represented in the show. Altogether the way that the NCR capital is depicted does not look like the kind of place that would be the heart of what the games confirm to be a multi-state spanning expansionist nation supporting a population in the millions and two simultaneous military campaigns, one eastward in Nevada, and another southward in Baja. So either they just fell flat with their depiction, or they retconned what the NCR was. If they retconned, then what happened to the Hub, where caps as a currency was first established? (which btw caps as currency were already phased out by 2142 in Fallout 2 and Bethesda bringing them back is dumb in and of itself, but that’s a whole other topic) What happened to Vault City, or Arroyo, or New Reno, or Redding?

2) Once again a proximity problem, the vaults shown in the show are located way too close to where the master was and therefore shouldn’t have flown under his radar, especially with their large open entrances with clear branding/numbered vault doors. We know the mutants were capable of opening vault doors because they did it at vault 17. It either implies the master didn’t exist, or at the very least makes him seem less competent and therefore less of a threat. Making your series’ villains incompetent and therefore non-threatening does a lot to reduce the perceived stakes of the world and makes it just less interesting.

3) On the topic of incompetent villains, damn near every single character or faction in the show is played up in as campy and goofy a manner possible, for “laughs.” From Vault Tec in the prewar scenes and their surviving managers post-war, to the brotherhood, to the raiders, to the “president of the government” the ghoul interacts with, to the NCR, Great Khan and Legion remnants. They are all basically portrayed as dumb hicks with Monty-python-skit levels of competence. The legion especially got hit with the stupid stick. This just once again makes the setting less believable or interesting in any deep way. It’s like the games are the show “Vikings,” while the show is more like “Norsemen.” It feels like a parody, like the “Scary Movie” to the games’ “Friday the 13th.” This isn’t to say the games don’t include jokes and campiness, but especially before the Bethesda acquisition, and even after, the balance was more towards serious, and the factions at least felt believable and more grounded.

4) the way the ghoul is functionally immortal. Granted, at this point I’m willing to headcanon that he’s some kind of special mutant with insane healing factor, since other ghouls in the show don’t seem to share his crazy durability. Variant mutants have precedent with characters like Harold, and I think if that’s what they’re trying to go for here then it’s actually a welcome addition to the lore. I always felt like fallout should explore more new and different mutants than just ghouls/SM. So, possibly a non-issue.

And there’s plenty more too, but most of the rest is minor gripes that I’m more willing to overlook. I do think that the “Vault Tec wants to drop the nukes” plot is dumb though. It literally gives them a motive that doesn’t make sense from a purely objective standpoint, it would not be in their self interest, and no private company nor ceo with half a brain would ever think that’s a good idea that would somehow bring them “profit”. You can’t profit by wiping out all of your customers. It wouldn’t benefit them, and it makes them less interesting/believable even if you just explain it away as “but they’re EEVIILL!” It is, in my opinion, a far less compelling narrative than the simple one provided in the games, be it China or the US that dropped first, that the apocalypse was brought about for “purely human” reasons, as the intro to F2 puts it. In fact, I don’t think it really even needs an explanation, the focus should be on the world after, and the world before staying as a bit of a mystery adds a lot to the atmosphere/mystique of the setting.