As for the Hakunin telepathy/dreams or the silly ghost story and locket quest, Fallout 2 could have done without that.
My personal explanation for the dreams and ghosts were hallucinations. The Chosen One specifically alludes to Hakunin having left an indelible mark on the youth through the use of hallucinogenic herbs, so while convenient that the Chosen One would receive these visions (specifically the one when the Enclave attacks), the knowledge that his village is proceeding closer to its demise the longer he takes is not a secret to him, so the visions could have progressed simply as a result of his subconscious reminding him to hurry the hell up.
The ghosts are a little less likely the result of hallucinations (playing with the RP, there is a SECOND ghost as part of the restored content, so it serves to reinforce the idea that there were no singular anomalous encounters in the game, as originally planned), but they still can be somewhat explained by the fact that, however sophisticated and intelligent, the Chosen One is still a tribal, raised on tribal superstitious culture. Some of his dialog clearly reinforces that despite his (potentially unusually worldly) knowledge, he is still subject to flights of fancy... or he's just being a smartass. But still, the former provides a potential explanation for why hearing ghost stories might cause them to think they've seen a real ghost, thus the quest. However, the events progress in the opposite direction, in the actual game. Rather than hearing about the ghost and eventually seeing her in the middle of the night, you have to see the ghost then ask Mom and other characters about it. (In the RP, the second ghost progression is reversed, depending on the time of day you interact with various characters. You can hear about the ghost that spooks the shaman, then afterward see it for yourself. Again, possibly the result of the Chosen One himself getting spooked.)
If all instances of ghosts had the prerequisites for "unlocking" seeing the actual ghosts were first met by hearing about it, I think it would work much better in the setting of the game, cause then superstition and scaring yourself into believing you saw what you believe you saw is an easy connection to make. *COUGH* Corrections for RP 2.3.4 maybe? =D *COUGH*
Oppen also offers a fairly acceptible explanation to the supernatural elements of the game:
TBH, the existence of psychic powers in Fallout 2 doesn't surprise me that much, considering there was psychers created with the help of FEV in Fallout 1, and the explosion of the Mariposa Base could have sent some FEV into the air and have unpredictable effects on the population in low doses. As long as there are few of them, I think they are believable. Now, if you create a whole town of psychers, you better make the explanation yourself instead of making the fans do your homework. But one or even two in the whole game, after 80 years of possible interaction with airborne FEV, believable.
But, remember, my original point was, REGARDLESS of how unbelievable the ghosts or visions may have been in FO2's setting, THEY were the more unbelievable aspects of the tribal-related items. Much more so than Arroyo's regressive and superstitious state. As Vault Maker EXCELLENTLY explained, it's really easy to reach that point, and the logical causes for some of those changes make perfect sense.
So, all in all, despite many fans' complaints about FO2 breaking away from the series' science fiction roots and delving into absurdity and fantasy and clashing with the original's aesthetics- whilst an understandable complaint, and their reasons for feeling as such it easy to see -it can still be noted that the setting still fits into the established themes of the original equally well!
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Except for Chuck Stogers, anyway.