The chosen one was raised in a village that could have transmitted the memory of vault dwellers and that do have contact with other cities. They could have extended more into that, but it isn't like they were totally isolated. Beside, you DO need months\years to improve your skills. Experience earned to doing a lot of things emphasises the time you spent to improve your skills. While leaving Arroyo, you are not the best scientist in the world, you cannot charm people like you had 300% speech and most human raiders can singlehandled obliterate you. It is not like Fo3, where you can destroy an entire gang of raiders a few seconds after you left your vault.
Of course it isn't like f3 but that's beside the point.
About the rest of your points, i think you're being too forgiving:
The arroyo tribals
could have transmitted the memory of vault dwellers and kept contact with other cities, i guess, but there's no indication of that whatsoever.
There's no gun on the village for example, yet your character can have guns tagged. We could assume that there were guns in the village or that he/she had some contact with the outside settlements, but the story plainly contradict this. And that's just for small guns. When you tag energy weapons, science, big guns, doctor etc there can be no logical explanation for the "chosen one" knowing these things no matter how you strech it.
And yeah, it's not 300% but a tagged skill can be 40-50% at game start and easily up to 70% by the time your character leaves arroyo.
Furthermore, the dialogue is somewhat inconsistent. In some cases the dialogue ( even all available choices for a particular option) indicates that the character is an ignorant tribal to the point where roleplaying otherwise is rendered meaningless. Remember the sherrif in redding asking you to kick a lady off her house? If you want to pay her rent yourself instead of kicking her out, you're forced to chose the line " i'm the chosen one, i don't need any money " to which she replies that she wouldn't like to take the money of someone touched to the head.There are many moments like this.
And yet in other places the character seems far more knowledgeable and less "tribal".
All these things of course, even arroyo itself ( hakunin, the elder etc ) are meant to be funny and not consistent. Like, the elder is literally just the daughter of the vault dweller, so why is she speaking about chosen ones and holy gecks etc? And while they are hilarious, i can't help thinking that fallout had a more interesting world that could be taken seriously and that also allowed deeper roleplaying - even if it had fewer options.
I do like many things F2 added to the lore though, like NCR, VC, The Enclave, in fact i consider them as
fallout as can be. And it's a great game as a whole, to be sure.