Alright so I'm going to include a lot of information that many of you will already know or will seem obvious after I say it, just a warning. This is also based upon the idea that you're living in the USA which many of you aren't.
First let's take a look at our two currencies and why things have value:
Membership - This means one (or two) months of double experience, and a 3x shiny chance. At 6 tokens or $6 a month, this isn't hard to understand because for anyone with a job, and a bit of disposable income, who spends a reasonable chunk of time on the game, this means getting to your goals 2-3x as fast (depending on your goal.) Since even the lowest income in the USA per hour of government approved work and pay, is around $6.50, this means that for an hour (and maybe another twenty minutes after income tax,) of pain or whatever it is you do as a job, you can make every hour on PWO many times more effective, while not taking away any fun out of the game, because you're still putting in the "work." Since we're already on the topic, let's now visit the poke'bucks side of this. 20 million. How much is that? As a new player, I have no idea how much it is to the rest of you, but that seems like a lot. However, given the advantages it provides, and how much more effective it makes your time, if you do happen to have an easy way of making a lot of in game money, it's really no big deal to drop this on something that is this high in tangible value. The tangible part is the time spent.
Various Levels of Rarity in Pokemon - So, depending on how rare a pokemon is, presumably it's worth more regardless of in what currency because it'll take more time to catch it. Simply put, if you aren't all that fond of spending hours looking for that Horribly Rare pokemon and you make more than that pokemon's value in standard $ wages for the same amount of time it would take to find, it's worth purchasing with real money or tokens. So if that's the case, why is it that more of these aren't sold? Surely more people make enough money that it would be worth it by that standard. However that's not actually how value works here, because if people didn't like finding rare pokemon, they probably wouldn't be playing this game, and even if they did play the game, and hated hunting for pokemon anyway, they have to grind. So we take in the enjoyment factor of their job, the enjoyment factor of the game, and how likely they think they are to encounter that pokemon while naturally grinding. Now everyone will have completely different answers for each of those variables, but the answers actually aren't all that important, we're just showing what's involved in each person's thought process. I should probably also mention that some people think that they can make enough pokemoney (through selling pokemon or grinding, doesn't matter) to obtain these even if they don't naturally encounter them.
Uncatchables - This is where things actually simplify. We can remove the fun of the hunt and enjoyment of the game factors here, because they never come into play. There is no way to obtain these unless you can purchase them with tokens, or from another player who has done so. For every pokemon of these types, money has been spent, and all we care about is the first two transactions. The RMT (real money transfer,) and if it then get's sold for pokemoney.
The initial purchase is all to do with two questions, only one of which is applicable at any one time:
1. Would I work my job X time for this pokemon.
2. Would I work my job X time for the pokemoney this pokemon will bring.
If the answer to number two is yes, then the purchase is made and the 2nd buyer gets to ask a question:
1. Would I work this game X time for this pokemon. - The problem here is that in this question X is not known by the person buying the pokemon. They can only guess or estimate.
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Now I've skipped any translation of currency, and switched it over to time because it's more consistent. None of that actually maters anyway, because those aren't actually the questions. Pokemon is just a filler word. What we're really asking is "Would I work ________ for this amount of desirable." And this concept applies to above as well, with the membership. I'm sure that up to this point, almost none of what I've typed before this paragraph really even matters, but it's there so that you can be lead into this next part, and that we are on the same page.
Players control the PokeCurrency values. Players Control the amount of desirable. Players do not control the "real currency" value. Naturally because different parties disagree on what each value is, there is discrepancy. Sorting people into the three groups:
Real Currency Controllers - Game Staff.
Poke Currency Controllers - Players as a whole.
Desireable Controllers - Players as Individuals.
Naturally the game staff has a certain amount of control over all currency types, because they can make decisions like making X object stronger or rarer (and thus more valuable,) or increase the amount of currency going into or being taken out of the game, but the direct control at the level of real currency control just isn't there.
Players as a whole find membership very valuable. Game Staff do not, they find membership is more valuable if more people can afford it, because it has an infinite supply. Players individually will disagree a bit on the exact desirableness (that's why not everyone has it, and not everyone is without,) however Players as a whole is loosely based on players as individuals, and the fact that it is in fact desirable to anyone (regardless of by how much,) means that it does have great value. Like food, everyone wants membership, it's just how badly do you want it?
On to Porygon! Players as individuals do not find porygon to be of great desire. There are players who flat out don't want it because it would take up box space and provide nothing in return (despite infinite box space having too many pokemon to go through can still be a hassle.) Players as whole (due to players as individuals) do not find porygon to be of high desirableness. Staff however find it equally as valuable as membership because it is equally easy to produce, and give as membership is. Staff has set a minimum cost on things of this nature.
This all, the whole situation is the equivocation of books. Assume you have two books by the same author. We'll use Orson Scott Card as an example here. Assuming they have the same number of pages, Ender's Game, and Ender's Shadow (two books by the author) have the same printing cost. They have the same shipping cost, so naturally the have the same total cost. However, the contents of one (let's say Ender's Shadow,) are better, and make for a much better read. Since they are the same cost to make, the publisher decides to sell them for the same price. Naturally more Ender's Shadow is sold. Now, there is demand for the book to be available for polish money as opposed to USD. Because it's not the publisher selling the books in Poland, and they're being resold, initial price, and exchange rates are ignored. Instead the reseller simply wants to make a profit over what he spent on them in his native USD. He knows that Ender's Shadow is better, so it will sell better, so he can sell it for more, so be buys more of it, and sells it, and makes mad profit. The Publisher never adjusts their prices, because they dont know what is going on, or how to take advantage of it.
This whole situation actually makes perfect sense. The token price of Membership, and Porygon, is simply wrong. Either membership can be sold for more, without dropping profit, or Porygon can be sold for less, while increasing profit. Because there is no way to directly purchase Poke-Currency, there is no regulation on the value of things directly. If you want to fix this "issue" you need to use one of these two solutions:
1. Find a way to directly control value (such as put a hard minimum on value, or create a direct way to buy poke-currency.)
2. Adjust your current view point of the value of various things, so that they more closely match those of the players as whole, and players as individuals, and in adjusting your viewpoint, adjust your prices.
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Now maybe someone else can word it better, or shorter, or something like that, but I've answered your question. Perhaps not in the way you want, or wanted to hear. Maybe it's not the answer you were looking for. I don't expect the S Alakazam, because you said it with the assumption that your question couldn't be answered, however if you're feeling kind or generous, I wouldn't be opposed to receiving one. I can assure you though, I'm more fond of Aron, shiny or not (cant trade anyway, so it's not like I could sell the Alakazam regardless.)
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I see some people saying that it's supply and demand, the reason this isn't exactly right is because both have a presumably infinite supply, and if you demand it, you can surely find someone who is more than willing the supply it. Supply and demand is more about ratios than it is about actual numbers. Few people demand porygons so I'd imagine few people buy them. Many people want membership, so many people buy them. If this was strictly a supply and demand issue, as few porgyon or memberships became available, they'd become more valuable. A lot of time the simple fact that there isn't much supply creates a large amount of demand.