I think it’s a tough question. There are mons GameFreak clearly tried to market, mons that I found through osmosis before I played the games, mons that stuck out to me when I played, mons I’ve seen my peer group and students talk about it, so on and so forth.
Maybe as a consequence of Pokemon Go, but over the years, I’ve heard constant mention of Rayquaza. Perfect IV Rayquaza, Shiny Rayquaza. A lot of memes about that intervention between Kyogre and Groudon. Out of all legendaries, it and Ho-Oh stand above the others, and the latter only bc of that scene in the first anime episode.
Rayquaza is very consciously gatekept in Pokemon Go and this has definitely artificially increased its rarity. One would expect it to come alongside Kyogre and Groudon but it generally doesn't - Groudon and Kyogre have been available on two occasions this year, whereas the last two occasions Rayquaza was available were 2023 and 2021 (edit: my bad, forgot there was a single day of availability for it this year - albeit in time-limited extremely difficult Elite Raids which could only be done in person, which basically supports my point about it being artificially rare). It hasn't even been one of Giovanni's shadow Pokemon yet.
So this has created a sense of excitement and scarcity around it that not many other species enjoy. Looking at Bulbapedia's availability list for legendaries in Go very nearly every available species has been in raids this year (the Johto trio and Mewtwo via shadow raids, which for some reason aren't counted on that list) - the only ones which haven't are the Swords of Justice, Deoxys, Hoopa, and Armoured Mewtwo.
But overall, I never got the impression Rayquaza was vastly more popular than Groudon or Kyogre - it's always seemed like a relatively even split to me. Rayquaza occasionally nudges ahead depending on the poll you're looking at, but Kyogre was definitely more popular at various points.
I’ll also say, Gastly/Haunter were in part shown off with the Silph Co lens, they weren’t some regular route pokemon.
I feel like Gardevoir is in some weird zone where people clearly like the design and know it, but it’s such a target for jokes about it being sexualized that it’s hard to treat it “seriously” like other popular pokemon. Vaporeon suffers from this too to a lesser extent.
I can honestly say that only terminally online people think of Vaporeon as sexualised, I have only ever seen that sort of content coming from really obscure corners of the fandom. Like even just scrolling down Google images there's only one picture of a humanoid Vaporeon from someone's deviantart and it comes off less as "sexy Vaporeon" than just... generic anime human Vaporeon, which I've seen done for dozens of species.
Gardevoir sure, to a degree, but even then most people's default reaction isn't that. The only Pokemon I've ever seen "casual" fans react that way to is Lopunny.
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