I think you make a very good point with the Cap City numbers, and they are an important piece of the popularity puzzle, but when considering something as nebulous as popularity, they really are only one piece. They give us a clearer picture of what shop owners expected to sell, but that's not the only thing we should be considering. If that were true, then Spawn would have been the most popular comic book character in the world at one time. But of course, this has never been the case. Phil Collins sold more albums than Madonna in the 80s, but who had the greater cultural impact? Who would 9 out 10 people tell you was actually more popular?
Spider-Man is streets ahead of Batman and Wolverine in merchandise sales, for as long as I can remember there has always been a general consensus that Amazing is the most collected back issue title, Spider-Man 2002 sold more tickets than Batman 1989(my guess is most 35+ year old collectors would tell you Bats 89 was a cultural event and Spidey 02 was just a popular movie), and if we scan the box office this century - when all three had simultaneous film careers - Spider-Man comes out ahead there too. But what percentage of fans would vehemently argue that Wolverine is the most popular character of the three? Among collectors, especially using sales to comic shops as the criteria, I could hear that argument. It's wrong, but I'll allow it.
What I'm actually suggesting is that the Michelinie interview, and merchandise sales, and back issue sales, Halloween costumes and 5th grade lunch table discussions all play a role in determining popularity, and GeeksAreMyPeeps and Peter Park also make some good points in this regard. I believe you originally said "until Venom became popular in 1993" and that can only be proven to a certain degree with numbers alone.
For instance, Marvel Diamond/sometimes-White-UPC issues should technically not be referred to as Whitman issues because, after a decent amount of investigation and discussion, we have definitive proof(unless I'm misremembering a Soapbox where Stan refers to them as Curtis issues separate from newsstand issues - someone check Snopes) that these comics were also distributed at shops and not exclusively in 3 packs. This wouldn't be the end of the world if someone got it wrong, but I would rather have a clearer picture of how things actually went down than not, so it's better to pass on accurate info. Venom's popularity before 1993 is a different question and can't be conclusively proven(nor does it need to be) any more than we can prove that Spider-Man is more popular than Batman, who is much more popular than Wolverine.
Quick tie in to the actual topic - If we aren't talking price, then I think Amazing 300 is the most important comic of the Copper Age (BA 12 misses the cutoff) because it introduces Spider-Man's Joker. I personally prefer ten other villains but none of them can support their own series of films, line of toys, etc. The Turtles should always be more valuable, but I'm predicting they continue to hang around in pop culture mediocrity while other characters grow in popularity.