This topic of Legendaries happens to coincide perfectly with my unpopular opinion - I really dislike the depiction of Legendaries as godly, one-of-a-kind beings. While I think Gen 4 is when this idea became solidified with the gods of time, space, and uh... actual capital-G God in the form of Arceus, it largely has its origins in Gen 3 with Groudon and Kyogre.
Generation 1's legendaries were simple, yet effective. The legendary birds were simply very rare beings, associated strongly with their respective elements, but not necessarily being deities of those elements. They were elusive creatures that you'd be lucky to find once in a lifetime - and it so happens that the player character does. Mewtwo, on the other hand, is closer to a god than any other Pokemon at this point - but this is deliberate, as it is a man-made mistake that has its power by accident. Mewtwo is a testament to what happens when man tries to play God, and that's what makes it such an iconic Pokemon. The imagery of Mewtwo standing in the lab it destroyed in the first movie, or tracking it down to Cerulean Cave in the games, made it seem larger than life in a way that no other Pokemon could attest to. Similarly, Mew, as the very first mythical Pokemon, was so rare that you simply could not encounter it in-game by any means other than an event.
We can see that Gen 1 introduced the 3 types of legendaries, which the series very rarely strays from. You have lesser Legendaries, represented by the birds, greater Legendaries, of which Mewtwo was the only one, and Mythicals, which was Mew. This in itself is a good balance; not all Legendaries will ascribe to the same level of power, so it serves to distinguish them from each other. Gold and Silver continued this balance, though notably, it was the first pair of games to use Legendaries for promotion's sake. Otherwise, they were largely similar to Gen 1 in how it treated legendaries, though notably, Ho-Oh and Lugia were natural beings. Ho-Oh in particular is woven into Johto's lore very well, and truly lives up to the name legendary - it created three new legendary Pokemon from nothing, and can only be found when you come to possess one of its wings. If you ask me, Ho-Oh and Lugia are the best portrayal of greater Legendaries we've seen in the series; they are Pokemon of great power and mystery in equal measure. The anime even depicts a baby Lugia, showing that while Lugia is a rare creature, it is not a wholly unique one.
From Generation 3 onwards, legendary design quickly escalated in terms of scope; perhaps out of a perceived sense of needing to make the next generation bigger and better than before, or maybe just because cool Pokemon do a better job of selling merchandise to 12-year-old boys who've outgrown the cutesy Pikachu. Groudon and Kyogre make the land and sea their domain, Dialga and Palkia control the fabric of reality, Reshiram and Zekrom are the embodiment of truth and ideals, Xerneas and Yveltal govern life and death, so on and so forth. I don't believe these concepts are bad in-and-of themselves, but being unique deities that lord over these powers is. It's been a running joke for years now that a ten year old can put God in a tiny ball, but let's just take a moment to think about how absurd that really is. The relative simplicity of Legendary Pokemon that existed before is now quite gone; no longer are they simply rare creatures, the logical extension of a game where the focus is on capturing and training these rare creatures, but actual deities that lord over all other Pokemon. It also presents some very odd lore implications; having legendaries recur in so many games (understandable, for the sake of Pokedex completion) means that these one-of-a-kind creatures are appearing in many different places at once. ORAS and USUM get around this by having these Pokemon come from other worlds entirely, but the Crown Tundra brings these issues right back by simply having them live in the Great Basement of Galar. These inconsistencies disappear if they are simply very rare Pokemon that only the most dedicated, talented, and perhaps lucky trainers will ever find.
I can't believe I'm quoting Ghetsis with sincerity here, but I think he says it best: "A Pokémon, even if it's revered as a deity, is still just a Pokémon." In my opinion, having legendaries exceed the capacity of a 'normal' creature so much does a huge disservice to how Pokemon should be designed. Ironically, expanding on lore using godly Pokemon makes the world feel smaller, rather than bigger. If they are truly gods, how are they defeated with (relative) ease in a battle? You can always say that they're holding back for the sake of competition, or they're restrained by their Poke Balls, but at this point we're using headcanons to write around inconsistencies. I see nothing wrong with legendaries being closely associated with certain attributes, nor being beings of great power, but having so many legendaries and having them be so great in scale makes the Legendary roster feel bloated. Indeed, this is a problem that game designers now have to deal with; how can you have every legendary be catchable in every generation without it becoming boring? The mystique of Legendaries is gone in favor of making cool Pokemon without substance.
tl;dr, since I wrote way too many words on this: Legendaries being gods rather than 'merely' strong and rare Pokemon undermines both lore surrounding Legendaries and game design.
