I always love seeing threads either criticising the originals, or complimenting the newer games. More often than not they result in civilized discussion, whereas if you showed an upopular opinion on pretty much any other Fallout fanbase they would say something among the lines of "STFU AND ENJOY THE GAME!"
As for your question, while I certainly see where you are coming from, you've got to remember that each of the negatives is kind of subjective, and there is a flipside for everything, so whether or not something is overrated highly depends on the player.
poor graphics (even for the time,)
It is incredibly hard for Isometrics to have good graphics. Look at Tyranny for example: Probably the newest Isometric out and it is barely any better than Fallout Tactics.
And besides, sometimes in games, when the graphics are decent, you are distracted due to too many things at once, and have trouble figuring out what everything is. In the original Fallout games, the art was just minimalistic enough that you could easily make out "Poor looking-guy", "Poor Looking Girl", "Guy in Suit", "Guy in Power Armor", "Zombie type mutant", "Big Green Muscly Mutant wearing rags as trousers". And for me anyway, I kind of focused a lot more on the dialogue because half the characters looked the same.
Not to mention how creative the art style is, with all this clunky looking technology, and these figures that look like they genuinely are from a new world, and not covered in Pre-War technology, and the whole Gothic style of buildings. I think that by improving graphics, you lose those aspects.
I'll admit, the mechanics are a bit shit, but they work. Even if they work very clunkily, they do allow you to customize your character and experience greatly. As for the combat, while most people say it's boring and repetitive, I would have to personally disagree. I really enjoyed the gameplay of FO2 especially. Like when you come across Raiders, and you take this whole risk of "Fight or Flee", and how there is always a risk of one of you landing a crit and insta-killing the other, I found it really tense, and with more challenging fights like the New Khans how you come up with your own tactics to fight them.
overall lackluster atmosphere
Lets for a second compare this to the modern games.
Fallout 3 occasionaly has a semi-dark atmosphere(Dunwhich Building for example), the rest just seems kind of dark and gritty in a non-atmospheric way. I never thought while playing it "Oh this is a dark atmosphere", I always thought, "God, another town with a depressing backstory, why can't anywhere have a happier theme to it?"
Fallout New Vegas feels very much Western, which is good, but it feels JUST Western. You don't think about how much the world has changed, you just think of it as being the traditional Cowboys VS Indians story.
Fallout 4 - I don't think it really has an Atmosphere. Gives too much of a pre-war feel to feel like the originals, and is nowhere near as gritty as 3. It has a kind of British feel to it, and feels very colonial, but that's probably just because Boston. Apart from that the atmosphere is kinda meh.
As for the originals, I always thought the atmosphere was quite good. Fallout 1 has an atmosphere of a world that has just fallen apart, and is only just being put back together, and you see all these communities starting to rise, each with their own flaws. It also has a kind of desert feel to it, with all these desert communities, which I think is quite good.
Fallout 2 has this atmosphere, that the only other game I think has been able to do effectively is Morrowind. It kind of feels like you are truly adventuring and exploring the world. You come across all these strange places, and the world feels kind of alien but at the same time still familiar. With all these Tribes, and the Slave Trade, as well as NCR expanding, as well as it kind of felt like it was this entirely new world, which was exotic, but at the same time resembled
what you already knew. Almost like a Fantasy game, but since it was set in a world with all the history to it, it kind of felt more real.
Almost every town had me wondering what I was going to find, and thinking how strange everything seemed, but not to a degree where it seemed unrealistic(*Cough Megaton being built around a f*cking Bomb*)
Also, it was one of the few games where I probably felt exactly how my character feels. Seeing this map with only 2 towns, and that being all the world you are aware of, everyone talking about all these towns as if everyone knew where they were, but you being an outsider having no idea, and while following the trail for the G.E.C.K and heading from Arroyo to Klamath to Vault City to NCR, it felt like you genuinely had been on this great long journey, and that you were in control of it, not following a linear questline.
Fallout 2, in my mind, suffers from a rather lackluster story that unfortunately permeates the entire experience for me.
I believe I have already explained why I think this is wrong above.
Anyway, if you feel the newer games are better, that's OK, it's a subjective opinion. Most of the aspects you mentioned aren't a matter of "This is better in this" or "This isn't as good as in this", every difference between The Originals and The Moderns is a two sided coin.