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I remember watching a video reviewing the Hoenn games, I think (gen 3 and 6). At one point the guy brought up how the appeal of Groudon to him was that it wasn't world-ending, it was just a beast with a unique ability that made people flip shit (causing droughts). It makes it a lot more 'legendary' to not be able to really comprehend Groudon's powers until you catch it and can read the Pokedex entry for it, presuming it's your first go on the game. The Pokemon world is 'magical' to our standards, but there should be realistic limits set to make it all believable... in a sense. As in, if our universe has a God, why in hell would they let themselves be known (debatable, the God - Arceus - sticking around in the early ages to be worshipped before man and poke-kind could become powerful), and especially be open to being attacked and captured?
TL;DR: Legendary (and mythical) Pokemon shouldnt be able to be world-ending god beasts because that breaks realism (the pokemon world is literally our own but if there were magical creatures. the timeline needs to be similar, as in, nothing TOO BIG in change) and the sense of wonder and intrigue Legendaries are *ideally* supposed to convey (this pokemon Is GOD! hey kid, do you want to OWN GOD? this other one can control time, too!).