San Fransisco. Definitely.
San Fransisco feels kinda bizzare in context: it's completely unconnected to anywhere else in the game. There's just a bunch of super-high tech Shi working on genetic engineering without any real statement of how they're able to do all this, and then there's the Hubologists who are basically just "Scientologists but in Fallout" which isn't a bad premise, until you realise there's not really that much more to them.
They're repairing an entire spacecraft ffs, and have access to high-end energy weapons, power armour, and yet somehow this is never really explained in the game. They're just a bunch of werird cultists who somehow have access to the utter height of pre-war technology. The only explanation given is "They have an eccentric scientist helping them out" which is kinda dumb. These guys are supposed to have the capabilities to repair a shuttle, which with the help of the Chosen One works. Granted they die regardless, but how the fuck do a bunch of Wasteland nobodies have access to an actual working space program?
Take the Salvatores as a contrast: they have high-access energy weapons because they're explicitly trading with the Enclave. Getting access to high-tech anywhere else in the game is a matter of having availability, yet these weird nobodies have access to it for no logical reason.
I also don't think it's adequately explained why the Shi, who are extreme isolationists, let a bunch of outsiders have access to some serious pre-war stuff. Like, ok I can somewhat see the Vagrants moving in to the Tanker and the Shi figuring "Hey it's just a ruin, who cares", but the Hubologists have access to what's most likely a pre-war bunker. Why?, Why would the Shi just let them move in there?
The premise isn't bad: the Tanker Vagrants, The Hubologists and the Shi forming the power structure of San Fran, but it feels like in execution it's done really poorly, because it's clearly rushed for time.
for official location, Gecko or Redding I guess. I don't find these places very interesting.
I like the sleepy gecko trapping village where the people there aren't tribal but still very low tech and primitive, it's nice to see an average town, but yeah it's pretty understimulating.
I'm biased in favour of Fallout 2 here, but I think these towns are great. IMO, towns don't need to have some unique far-flug premise, they can still tie in to the world in an interesting way.
Gecko might seem underwhelming, but honestly it's one of those towns that doesn't just exist as an isolated thing, but rather in direct contrast to Vault City. Vault City hates mutats and sees Gecko as an abomination, however nonetheless they are inherently reliant on one another: Gecko's polluting the Groundwater because they don't have the correct parts to get the Power Plant in working condition, whereas Vault City DOES have those parts, so unless they co-operate they can't deal with the crisis.
Moreover, Gecko hopes to optimise it's power plant so it can gain a position of power in the Wasteland selling power, whereas Vault City is unable to expand because it's Vault generator isn't enough to sustain it in the long term. Part of the fun in Gecko comes from it's connections to Vault City and how it's necessary for the two towns to co-operate in the future.
As for Redding, it's position as a Gold Mining town makes it extremely valuable in a wasteland where Gold is used to create NCR Dollars. The entire premise of the mine with access to extremely rare technology being taken over by Wannamingos, and none of the mines being able to take over is immediately interesting. Not to mention this is where the morality of the Jet crisis comes in: do you cure people of their addiction and let them get taken over by Vault City whereby the majority will never be full citizens? It reminds you of the significance of Vault City's medical technology.
Klamath is interesting not only because of it's unique array of characters that immediately get you accustomed to the types of people you might meet in the Wasteland. The town drunk immediately trying to scam you by pretending to be a greeter, the families feuding for control, the Irish Boxer who immediately takes the piss out of you, before realising you need help to survive in the wasteland.
But also because it starts to introduce the overarching economic system of the game: you have Indentured Servitude which immediately sets up the premise of slavery, you have the immediate suspicion of tribals, you have the Distillery in the Wilderness which is explicitly mentioned to be tied to the Wright families' monopoly on Alcohol over in New Reno.
One thing I do find kinda arbritrary is the fact that the people in Klamath know of the existence of both The Den and Redding, but only point you towards the Den. Shady Sands only really traded with Junktown and heard about The Hub in passing. It's never really explained why you can't go from Klamath to Redding, other than Redding being too high-level.
These towns might not be the most unique ones in the world, but they're ultimately tied to the greater conflicts in the wasteland which I think makes them interesting.