It vaguely fits with established Fallout lore. Some bits clash (some clash rather spectacularly, like T-51b Power Armor not enhancing strength at all), while some fit quite well.
The Vaults are generally good looking, but their layouts are completely different from those that were on the West Coast. Most of the stuff dealing with the Vaults fits well in the lore, too.
Actually, they mention how each one has a purpose and these ones have been designed around that purpose. Every Vault, of course had a purpose, but these ones reflect it in being purpose-built.
The DC super mutants, and their source, aren't really explained well enough to justify the clash between the lore and what is presented. Maybe I just missed reading some things in the super mutant's home, though. Why the DC super mutants became stupider instead of smarter when dosed in FEV is also never explained.
I always had the impression that the Super Mutants weren't very smart in FO 1 and 2 with the exception of a few, the sherrif of Redding for example (except when he shoots me in the back).
And the spread to DC, as I recall FO:T indicated that Super Mutants had spread as far as the Midwest at that point, if not further. That said, there is SOMETHING else going on for why the Super Mutants are so numerous. It IS explained.
For some reason, the Chinese had infantry in DC. I haven't seen a single explanation for that one yet.
Chinese Special Forces were deployed before, during, and after the nuclear exchange to the DC area to try to screw up the US. As things fell apart both here and in China, they were stuck. It isn't hard to imagine them here. WW2, Germans had spies in the US. US deployed Special Forces to Iraq and Iran and Pakistan in the real world.
The Brotherhood of Steel is annoyingly inconsistent with the original Fallouts - they're much too altruistic in this one, though that's explained by Elder Lyons being a wuss and everyone else following him.
I don't think it is inconsistent since the Outcasts are there. They obviously don't like what Lyons has done.
The Enclave generally fits well with established cannon, but you have so little information-exchange between you and them that it's difficult to tell.
There's zero explanation for why a high-tech research project was being done underneath the Pentagon, though. I'm not sure if that clashes with the lore or if it just clashes with reality.
Why? There was no mention of the Pentagon in lore outside of it being a decision center. The idea of there being sublevels? I bet there are sublevels and many to it. The idea of a lab there? Why not? If there isn't a research lab there, certainly elsewhere nearby. Why not move the biggest defense projects underground (after all schools did it, if you notice from exploring!). Move into the largest underground space the government has!
The visual style of things has changed considerably, and with absolutely zero reason why - Enclave power armor (which is, for some reason, worse than Brotherhood armor even though the Brotherhood people specifically state Enclave power armor is better) looks more like Tactics power armor, super mutants don't look the same at all, weapons look completely different, etc. The Sentry Bot has changed from a walking bipedal robot to a giant tricycle.
The Vaults also have guards wearing armor and such, which is a pretty big change from the originals.
I am not sure why this is a problem? Vault 101 has a special role and it needs to enforce that role. Consequently, they are better equiped.
I though enclave looked pretty similar to FO2, except the suits aren't as bulky, which is nice and better looking.
The storyline is just a mashup of the plots of Fallout 1, 2, and Tactics, which makes it rather annoying if you're too familiar with them. Way too many plot points were reused, though most were altered in some small way. I'm not sure if that qualifies as 'lore' though.
I think the idea is for it to be a mashup. We WANT the story to be built from FO 1 and 2. We want some ideas to be reused (BOS helps character in taking down some really [censored] faction.
Besides all of these things, it fits reasonably well in Fallout lore. Most of these changes aren't too annoying, and even with them I enjoyed the game.
Obviously, I think the game fits in very well. A lot of the lore and historical records you find are directly taken from previous games. It trusts FO1 and 2 over FO tactics with what is canon. In story and style it is more like FO1 than 2.
Additionally, when I gained access to 'Minefield' I found lots of houses. Some had notes from Vault-tec saying they won't be getting into the Vault of their choice. I went in one house, I found the husband and wife skeletons in bed with some stims of Med-X. They killed themselves. The skelton of their child was outside next to a tricycle.
Awesome atmosphere.