Alright, I'm going to take a deep breath here and exhale. Let's approach this again.
I reread every single one of your posts in this thread, Lance. The critique you appear to be making is that our analysis is focusing too much on individual cards rather than the strategic elements that go into them. Hypothetically, decks should be broken down into the schools of Magic: aggro, control, tempo, combo, etc. Lumping decks into an archetype like 'Shops' ignores the strategic distinction. Similarly, decks like Blue are typically strategically 'control, or 'tempo', or 'combo'. Correct me if I'm wrong, but I believe this to be the gist of you position. If so, I would say you are coming at this from a theory-based approach or an academic approach.
Where we differ is that we want our data collection to be useful. We want people to look at our breakdowns and do something with them. This can be adjusting their main deck or sideboard to contain more Dredge hate or more Shops hate. From that perspective, it frequently doesn't matter what the ultimate strategic goal of a deck is. Cards in Magic don't typically interact with strategies. There isn't a card in Magic that says "counter target aggro spell or destroy target aggro permanent." Cards in Magic interact on different axes: colors, permanent types, hand or graveyard, the stack. So what is useful is a breakdown based on these levels of interaction. While it might certainly be useful to include different cards against a Control Shops deck vs an Aggro Shops deck, it's a moot point when one strategic orientation is much less than the other.
Another way people use data is to make informed ban and restriction decisions. We know WotC does this although many players seem to make these decisions on a more emotional level. Sobeit. I don't believe we are tailoring our data to specifically favor or disfavor specific restrictions. We are simply trying to aid players in looking at the metagame in a way that lets them evaluate their opinions with regards to the metagame. For instance, people were clamoring for a Paradoxical Outcomes restriction immediately after Gush was restricted. While one could certainly argue that the card is non-interactive, it's a different question of how popular or unpopular a card is and how frequently decks with that card win. When you look at the data, decks with Paradoxical Outcome do not seem overly dominant when you look at metagame share or win percentage.
I think it's very common in science to do this. Start with the hypothesis: is there a correlation between smoking and cancer? Set up your cohorts and collect data on different groups, and you should end up with a study that answers your question, albeit with the usual statistical limitations, potential biases, and possible confounders. Is what's being done here dissimilar to a cohort study? Does it not make sense to look at Shops decks relative to the field to see if there are metagame or balance concerns with decks that play this card? Note: you could do this with Force of Will or Mental Misstep, but I'd argue that those cards are so prevalent that the statistics here simply do not matter. You either feel these cards belong in the format or you don't at this point. Whether they are 60% of the metagame or 70% really shouldn't affect anyone's position.
In conclusion, we are approaching the taxonomy of Vintage from two fundamentally different ways. You have a theoretical approach and we have an observational approach that is a bit of a mess based on trying to meet the different needs and perspectives of Vintage players (combined with limitations like our time and the available information). So if you can propose a question or purpose that we can change our classification scheme to provide insight into, we would be happy to do so. However, if you think that what we are doing is theoretically sloppy and inconsistent, and a more rigid approach would be better, we would be happy to share our data with you.