The fact that, up until now, there's been no 'Headscratchers' page for The Prisoner is a headscratcher. Seriously, people have created pages for animated credits to a quiz show, is everyone going 'The Prisoner. Yeah, all makes perfect sense to me'?
Perhaps people wouldn't know where to begin? As soon as you start to type about the finale, your mind seizes up and becomes a David Lynch film until you click back.
I'll risk it and ask the question that has to be asked. What the blue FUCK happened in the final episode?
It's metaphor for a person being trapped in Society and forced to conform to other people's desires instead of his own individuality. At the ending, Number Six realizes that he is trapped in an Epiphanic Prison even more so than a Literal One. It all makes perfect sense in a metaphoric standpoint, but from a literal one, well...don't even bother. At the very least, the Core Theme is about Individuality VS Collectivity, or a Man Against a Village.
If you count the comic book sequel, Shattered Visage (which got enthusiastic approval from Leo McKern and which McGoohan refused to condemn), "Fall Out" actually does have a literal explanation. It is revealed to have been a ruse on the part of McKern's Number Two that partially involved sets & actors and partially involved exposing Number Six to mind-altering drugs. It was an attempt to assault Number Six's very psyche and what finally broke Number Six's will.
Alternatively, you could check out the WMG page for more theories on what the heck happened in Fall Out.
It just bugs me that no one else mentions how hot Patrick McGoohan is in this show. Yes, shallow.
He works for whomever he perceives to be in charge. In "Once Upon A Time", Number Two says "He thinks you're the boss now," which pretty much sums it up. I think a more interesting question is why did Number Two pull a Heel-Face Turn after Number Six freakin' killed him?
I think Number Two ultimately blamed Number One for the whole mess anyway. It was obvious as of "Once Upon A Time" that he was growing to resent those he answered to, and at the end of his monologue in "Fall Out" he rages at Number One — even to the point of spitting in One's camera "eye".
Number Two is himself a prisoner; he just happens to be one of higher status. Nevertheless, he's come to resent being a prisoner.
Number Two was not only himself a prisoner, he also lamented his own breaking. Even in the spin-off comic, where he celebrates Six's fall, he deeply regrets it at the same time. Six is not a character easily explained; why should Two be?
This one's a niggle; for keeping track of work-credit transactions, they use little cards that vendors punch holes into; doesn't seem very efficient. Didn't they already have magnetic stripe cards in the 1960's?
The organisation behind the Village could be bureaucratic and slow to change things like that. Equally, it could be part of the whole 'retro' vibe of the Village.
While the technology for magnetic stripe cards existed at the time, it was far from widespread, and the audience probably wouldn't have known what it was. Also, it's not as inefficient as you might think. It's a cashless economy of not too many people, and presumably the cards arrive in the mail once per week. It's certainly less complicated and more efficient than distributing cash, and while centrally generating credits would be better it would also be extremely difficult in the 60's.
Given the general caliber of computer technology available, magnetic stripe cards would be essentially the same amount of work anyway. Records of earnings would almost certainly have to be kept in paper ledgers, and then the cards individually coded with the right amount. Compared to marking the right number of boxes on cards, it's about the same amount of effort either way.