This is needed. Great thread Doug, I hope that this will become a stable basis for the current metagame, and those in the years to come.
Us LC policymakers have run into problems with the lack of clarity on how to deal with non-Pokemon suspects. It seems to end up as trying to apply the characteristics of an Uber to something they were not designed for, a matter of what can only be described as personal preference for how the metagame should be, or simply saying that something with as wide ranging effects as Berry Juice should not be banned.
As for the specific "stock issues", I'm not convinced about several you listed.
I agree that the metagame should be "Competitive", however I don't see how this stock can be used positively in any discussion about specific rules. Unless you take the attitude that a luck based game is inherently less competitive (which is addressed by the "Luck" characteristic) then this seems to be largely determined by player attitude, not directly by our ruleset. Maybe it could be used as reasoning for cutting out ingame elements, but that's not something that anyone is likely to ever argue on Smogon. I could also see this being misunderstood and used in questionable situations, especially if it is mixed with the "luck is not competitive" train of thought.
The Variety and Balance characteristics seem like they are almost interchangeable, maybe could be combined? They both deal with not having a small number of options dominate, which allows more options to be viable. You say that one deals with "Overcentralization" and one with "Overpowered" elements, but the distinction between those two is blurry at best. Are there situations in which there is something that is "Overpowered" to the extent where we would ban it, but is not causing centralization (or vice versa)?
Stability is an interesting point, and one I have not often seen brought up. It relates more to practicality than determining the best possible metagame (whatever that means), but it does seem to be a valid point and maybe one that should see more use in discussion. Short term instability is not necessarily a problem, but if there are large constant shifts then players have to work much harder to keep up to date, and those producing strategy information have to concentrate on updating information rather than simply improving it which hurts quality.
I share obi's concerns about allowing authorial intent arguments to slip in, but that is probably a simple matter of slightly rewording that characteristic. I would also think that Adherence is not something that is optional, it is required. If we start intentionally making changes to Pokemon things are liable to get arbitrary and extremely complex very fast.
I'm also wary about including both the Skill and Luck characteristics, Skill is an almost unavoidable part of a game as immensely complicated as Pokemon and like the Competitive characteristic I could see it being misused. How much impact Skill has is also extremely hard to measure or control with rule changes. While I think that what was written for the Luck characteristic is much better than many attempts I have seen, I think that the best way to reach a "reasonable" level of luck is to ignore it. Attempting to control it, either to cut it down because some players dislike the effect it has on the metagame even when it does not centralize, or to bring it up because other players may think that the effect of luck has been artificially and unnecessarily lowered by things like the Evasion and OHKO clauses.
One important characteristic that you may have touched on slightly, but as far as I can see not directly addressed, is that there should not be any rules or bans without good reason. A simpler ruleset is inherently better than a more complex one, if Feebas was banned from OU for some reason then even though it would have virtually no positive effect when brought down, it should be. This rule also helps deal with suggestions like "Level x (less than 100) Uber is clearly not broken, why is it banned" or "Garchomp would be fine so long as we ban Outrage on it", which generally can't be met with arguments from any of the other characteristics (bar Stability at a stretch) and would result in endless testing and tweaking of the level the Pokemon until it is not overly centralizing, but no lower than is needed. Allowing low level Ubers would likely increase variety, so without a characteristic to explain why it seems crazy (or at least totally unfeasible) to most of us, we would be in a bad situation.
Once again, thank you very much for getting this together Doug, I may not agree with some of the characteristics you propose, but I entirely agree with the sentiment of having a set of "stocks" for people to argue from.
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