Heh, I see the point in some of the OP's arguments, but in others I see nothing wrong. About the wasteland feeling, that's really not what I deliberately seek, so NCR and San Fran don't hurt my view of Fallout 2. I seek good story and setting. And Fallout 2 provided me with those, also with a new post-apocalyptic mania, but that's beside the point.
NCR's existence makes sense, since the old institutions remain in the subcounscious of people, and that the work they profit from brings them power to choose a new society, San Francisco's Chinatown is a bit of a coincidence but altogether they're pleasant settings. Little towns awakening from the dusk of Atomic War, it makes sense that they would strive to reach back the old ways. Not that they'll ever achieve it, but sometimes it'll be remembered.
One of the reasons I liked Fallout 2 so much, way back then, were the turns in the story. Part of why we loved Fallout 2 so much at the time, but part of why we see so many contradictions now, comes from these story turns that they deliberately put into the plot. You're a tribal, you leave to Klamath, you find Vault 13 and BAM, it's full of Talking Deathclaws! You expected Enclave soldiers, vault dwellers, even NCR squatters, but not TALKING DEATHCLAWS! Honestly, I don't like it now but when I saw it for the first time I was thrilled. Seeing the Deathclaw appear as the Vault Door opens made me run like hell, but returning and speaking to it expecting it to enter combat mode, and seeing a dialog box pop up is historical.
I'm not saying it was coherent, just that such a moment will always stay in my memory due to the surprise it caused back in the day. But I agree, it's contradictory. The Enclave solution seems too, but it wasn't. I know that the Enclave said that the others were mutants, but that was just a hypocritical excuse for taking over the world, their true goal.
Fallout 2 violated the setting a lot, but the reward was an unforgettable experience. Could be done differently, but it's beyond discussion since it's good enough as it is.