I was never trying to imply that contradicting your own story isn't a problem. It is, and Fallout 3 does it a lot. I just think the significance of the issue gets exaggerated. People are often far less impartial and forgiving to a game's wrtiting when they dislike it for other reasons. The reverse is also true.
It annoys me that in Fallout and Fallout 2 radiactive goo glows green. Not realistic and immersion breaking.
It annoys me that the Gun Runners in Fallout are set up literally right next door a Deathclaw nest. Unrealistic and stupid behavior.
It annoys me that Caesar himself in New Vegas is set up within sniping and artillery distance from NCR territory yet they don't attempt either of these things despite being both desperate and capable of doing so.
Yet if you try to point any of those things out, people will be quick to provide an explanation because they actually like the underlying games. Nobody ever comes to Fallout 3's rescue however, since it largely dropped the ball on being a role-playing game.
Again, I'm not trying to say small immersion breaking details aren't problems. Just that when comparing them to games that have similar flaws, it's a little unfair. Anybody could go over Fallout, Fallout 2, and New Vegas with a fine enough comb or a small enough microscope and pick out things that annoy them. People just love to do it with Fallout 3 and Fallout 4 because those games infamously hated (with good reason).
I don't see your complaints as nitpicking though.
If people are quick to provide an explanation for those things, it means that the games offer some kind of way to offer an explanation. But Fallout 3 does not really offer an explanation for most of those "small" things people complain about.
For example I know why some things you complain about are like that in the classic Fallout games and FNV, I could be quick to explain why they are like that. But that wouldn't make them less bad for you. What I can't do is explain why Fallout 3 has most or all of those things I complained about in my previous post. And I play Fallout 3 regularly, and I did had fun playing it (but would have had more fun if the game didn't had all the small problems that really annoy me).
Also about "games with similar flaws" and "go through the other Fallout games with a fine comb". The problem here is that you would have to go through the other games with a fine comb (Fallout 2 is an exception), but in Fallout 3 you don't need that. It is all there straight in the players face mostly for no reason except "because".
Also everyone knows that Fallout 2 is full of stupidity, and I don't know many people who would try to excuse that stupidity (many even hate Fallout 2 because of that). But the Fallout 2 we got is not the Fallout 2 that Black Isle wanted to make, it is the Fallout 2 that they were forced to make in six months (actually 9 month IIRC, but Interplay counted the 3 months Black Isle was just trading ideas for a Fallout sequel before Interplay told them to actually make a sequel, as past of the development) while many people were leaving the company during the production of the game. Which is important to note, because Fallout 3 is the game Bethesda wanted and had all the time to make.
I am making this distinction because while Fallout 2 is full of stupid stuff, it was forced to have that stupid stuff, but Fallout 3 is full of stupid stuff but that was what they intended from the start. And I point out again that I don't know many people who wold try to explain Fallout 2 stupidity either.
Now, does this means that people who enjoy Fallout 2 and/or Fallout 3 are bad people? Of course not. Tastes are different. I like Fallout 2 and I enjoy Fallout 3 (specially with the improved engine and stability of FNV), I also like Fallout and Fallout New Vegas, the one I didn't enjoy at all was Fallout 4 because I can't get into FPS games.
I have nothing against people who have fun playing Fallout 4 either, or that don't like Fallout 1, 2, 3, NV.
Now, this is not relevant to the discussion. But I will post it here because I think it is interesting.
They picked green for the radioactive goo because that was the color of pretty much every dangerous radioactive material in all the entertainment in the past (books, comics, movies, TV series, etc) and because they had to come up with a color that would stand out and be immediately associated with danger. All using a 8bit 256 color palette: