Most of the time it's obvious that Gamefreak made the game with one legendary in mind and just kind of awkwardly crammed in the other so they can sell two versions. Ironically it's often the "non-canon" one that's more popular.
Johto: Ho-Oh is more important than Lucia in Lugias own game, however Lucia is one of the most popular Pokemon ever and Ho-Oh is kinda middling popularity wise.
Hoenn: Sapphire is so obviously the canon version it hurts. Ruby's plot is downright nonsensical at times with how Gamefreak put zero effort into rewriting the story for it. Gordon and Kyogre are both fairly popular, but Fug puts them both to shame.
Sinnoh: The only region where the third version is the obviously canon one. Platinums story is basically the actually finished story, with DP basically being a rough draft with no real version differences that ends abruptly with an interchangeable legendary. Dialga is slightly more popular than Palkia but neither is particularly big compared to the massive popularity of Giratina.
>Unova is strange because White 1 and Black 2 are the ones the story is written around, despite the fact you're supposed to buy the sequel to the version you bought instead of the opposite. Neither Reshy or Zeke are popular at all, though Kyurem is fairly liked.
Kalos: The funniest one, because the game is unique in that it's the only generation designed from start to finished around the third version being the true game, and then they never got to make the third version. So you have two games that far more than even DP are hinting at something more. And are themselves just plain rushed unfinished messes. Zygarde is the most popular, but again, didn't actually get his game.
Alola: Actually matches up. Solgaleo is both more popular and the one the story fits.
Galar: Zacian is so lopsidedly popular you feel bad for Zama, but they're completely interchangeable storywise in a game where the versions have no story differences.
Paldea: Mirai is more popular and canon.
