>>13580281Ah, I get your point. The storylines of the games from Gen III and up don't leave too much room for doubt, however. Oftentimes, the fate of the world seems to hinge on your success taming these beasts. Of course: perhaps Kyogre did not create the Earth's waters—but its mere presence can apparently still cause floods of biblical proportions. That's still pretty big.
Giratina, meanwhile, presides over a bizarre alternate dimension, shown to be very much real.
Ho-Oh's legend allows for some doubt; it presents itself mainly as a unique Pokémon which often perched itself on a certain tower, and around which legends were spun. You can investigate the legend and be rewarded with a special Pokémon, the true core of the tales told. This is much more subtle.
Mewtwo, too is a legendary Pokémon as I would prefer them. You learn about it from incomplete records, and it becomes evident that it is very powerful. So you can seek it out, challenge it, and with a lot of effort subjugate it—a proof of your strength, and a conclusion to an obscure chapter of history.
Quite a far cry from it being shoved in your face that this ruler of the elements is going to end the world unless you throw a Pokéball at it.