The main distinction you are trying to draw between types of opinions is just related to whether the opinions are rational. Basically, you like this variety of pie without a rational basis (e.g. you have not considered its nutritional value etc.) The only sorts of opinions we should be discussing at all here are rational ones because irrational opinions should be immediately dismissed. I support the definition of "overcentralisation" I do for a reason, not just because it seems better.
Your distinction between rational and irrational opinions is an interesting one that I'd like to explore further. I posit that all opinions can be broken down into component parts. These parts consist of one or more preferences and zero or more hypotheses. A preference in this case is something that either pleases or displeases us on a basic level, but that we cannot back up with facts. A hypothesis, of course, is a guess or belief about something that has an unknown boolean value, such as "A is true", "A causes B", or "If we do A, B will happen." Hypotheses can be supported by evidence. Preferences cannot.
An opinion that contains a hypothesis might be something like, "Garchomp should be banned." This can be broken down into these parts: "If Garchomp were banned, the game would be less centralized." "I prefer a metagame that is less centralized." The first statement is a hypothesis and the second is a preference. You
could say that an opinion is rational if the hypothesis is based on supporting evidence and irrational if it is not. However, the underlying preference portion of the opinion will always be 'irrational'. Things may work out as you predict, but that doesn't mean that everybody should like the outcome. Hence, there are no 'rational' opinions.
Your opinion is that we should ban as little as possible in order to make sure that there are at least X Pokémon in the top 75% of usage on Shoddy. If I'm not mistaken, you want this because you want simpler rules (a shorter ban list). However, you have yet to provide us with a reason that you want the rules to be simple. It could be that you hypothesize that simpler rules will make more users happy and you prefer more of your users to be happy. It could be that you hypothesize that fewer rules will minimize complaints and you prefer not to deal with complaints. I have no idea. Regardless, all of these opinions are reduced to an 'irrational' preference. Not everybody likes simple rules. Some people play Tic-Tac-Toe. Others prefer Double Fanucci. I enjoy the complexity level of Pokémon, and while I don't believe that we should be making additional rules for complexity's own sake, I have no problem with imposing bans that make the game more varied.
Your cutoff point of X≈50 is also arbitrary, as has been pointed out numerous times. If all irrational opinions should be discarded, why should we ban any Pokémon at all? The game will still be playable this way and the rules would be vastly simplified. 'Fun', being an intrinsically irrational thing, should not be taken into account.
Even the word 'simple' carries irrational preferences. I could argue that banning all legends and a handful of other Pokémon is no more complex than the individual ban list we have now. As someone who has played the game with a great variety of rule sets, I hypothesize that this would make for a much less centralized metagame without adding to the strict number of rules on the list.
Taking a step back, we could question whether a perfectly rational person would even play Pokémon at all. Does it help us accomplish our life's goals? In fact, our goals themselves are preferences. Even our drive to stay alive is nothing more than a very strong, hardwired preference.
In other words, everybody who plays Pokémon plays it for fun. (Yes, people who play to win are still playing for fun. They enjoy playing and winning.) To dismiss opinions that are 'irrational' is not only undesirable, but it will leave us with nothing to work with.
Man, that was long. Time to tackle the next subject.
Let's consider your analysis about whether this particular mechanic was "intentional".
Although the developers removed this mechanic from future versions, they left in the trade feature. The trade feature allows you to trade over these pokemon from the previous version. It is clearly intentional that you can trade these pokemon over. If the developers had not wanted you to be able to use these pokemon in the new version, they easily could have prevented them from being traded over. Since they didn't, they clearly intended you to be able to trade these pokemon over.
I doubt this is going to convince you, but it seems about as solid as your analysis above. The action required to block these "illegal" sets would have been very doable by a competent team of paid programmers, and if they had intended them not to be tradeable, they wouldn't be.
I actually think your argument about leaving in the trading mechanism is a very good one. However, when you look at it from the developers' perspective their decisions are easily explained.
Removing the trading function between Japanese and American versions would have been unacceptable. This international trading (and the Global Trade Center) was one of the much-lauded features of this generation of Pokémon games. Even if the developers had wanted to remove this in order to quarantine this mechanic, the higher-ups would never have agreed and the fans would have thrown a fit.
Preventing only the trading of Pokémon with illegal movesets seems plausible, but imposes strict limits on future versions. If the game were to contain an algorithm that finds illegal movesets like the one I'm developing, it would be able to detect and prevent the trade of Pokémon with these movesets. However, if a Pokémon were to receive a new move in the Platinum version of the game, this Pokémon could not be traded back to American copies of Diamond and Pearl unless and until this its internal learnsets were updated. I'm sure there are ways around this too, but you can see how it could quickly get very cumbersome. DS carts only have so much space.
It seems very likely to me that the developers wanted to remove this mechanic but did not feel that the cost was worth the benefit. Now it's your turn. Can you give me a plausible reason that they took it out of the non-Japanese version other than that they considered it a glitch?
I've been meaning to do this for a while myself (it's better than the incomplete hardcoded approach we have in Shoddy Battle now). Hopefully you will contribute this to Shoddy Battle (i.e. release it under the GPL or a licence compatible with the GPL) so that we have a better mechanism for verifying illegal movesets. Does this consider interactions with advance? (If it doesn't it will still be useful; we'll just maintain that part of the hardcoded list.)
Making my algorithm available to Shoddy Battle is absolutely my intention. I'm only too happy to provide it. I do plan to include 3rd generation support, although I have not included it yet. The main problem I've run into so far is getting the Pokémon learnsets into my program. For my tests I've been hardcoding them, and I'm thinking about using a .txt file to store it, but I'll see what Shoddy currently uses and try to hook into that whenever I can. (The algorithm I can handle, but interfaces are my weak point.)
Actually, what I am trying to convince you of is that you should like lemon meringue pie, not that you do. And if you just refuse to like it in spite of the arguments that you should, you are merely irrational. Of course, we are all irrational with our food choices. I only eat one meal a day for example, because I think eating is a waste of time. That is definitely irrational, but I prefer it that way and since it is something that affects only me it's acceptable to defer to an irrational conclusion. As for developer intent, I would like to show that you shouldn't consider it, not that at present you don't consider it. These issues affect more than yourself, so irrational opinions are not acceptable here.
I think lots of people do change their opinion on developer intent, perhaps by playing other games. There are lots of games where glitches are a key part of the metagame, and after realising how you are just limiting yourself by sticking to the developer's intention, you might carry that philosophy over to other games. I've known people who complained about "glitches"... until they played Mario Kart DS and realised that snaking, despite being universally hated by scrubs, actually made the game better, and then carried a more nuanced opinion on what should be banned over to other games. I'm not saying you should go out on play Mario Kart DS, and in fact you probably should avoid that game since it's crap. But I do think people's opinions on this can change.
You're arguing that I should like lemon meringue pie. To ignore rational arguments that I should would be irrational. My claim (as outlined above) is that there can be no rational arguments that I should like it. There could be rational arguments that I should eat it (nutritional value, etc.) in the context of my larger goals (not starving to death), but not that I should enjoy the taste of it. It seems likely that there is nothing I can do to improve my liking of it, so telling me that I
should enjoy it doesn't accomplish much.
The fact that this decision affects more people than just me does not invalidate my opinion. As I have tried to show, your opinions are no more rational than mine (nor could they be). What it means instead is that we should put it to a vote so that the majority of users have their preferences met. If there is a significant percentage of people on both sides of the issue, perhaps there should be two metagames and/or a test period for a change like this.
I do not doubt that some 'glitches' can make a game better. I hypothesize, however, that this particular change would not improve my enjoyment of the game. I still draw a distinction between an unintended mechanic and a game balance decision. I think there's a reason that Crobat can't learn Hypnosis and Nasty Plot and that Azumaril can't learn Belly Drum and Aqua Jet. These decisions are every bit as real to me as the decisions not to give Medicham Close Combat or Gyarados Brave Bird.
Side note: I too try to minimize the time I spend eating. In the context that this frees up more time for other activities, I consider it a rational decision made to help achieve my (irrational) goals.
I also feel you are limiting your appreciation of literature by focusing on authorial intent, and really it seems to me a travesty to impose one interpretation on a work rather than analysing the work for what it is.
You might enjoy
this classic essay on authorial intent.
You may rest assured that, for one reason or another, my stance on authorial intent does not carry over to my appreciation of literature. Perhaps this is an artificial distinction, and I do see what you're getting at. Just to nitpick though, what do you mean by analyzing a work for what it is? 'What it is' seems to imply that there is one correct interpretation that may or may not be what the author intended, but I think I may be reading too much into what you're saying. I'll take a look at that essay, though. Maybe that will clear some things up for me.