PokéBase - Pokémon Q&A
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Palkia:

Palkia, along with Dialga, may be based on the Shinto legend of
Izanami and Izanagi, who are said to have created one island with a
spear, erected a pillar on it, and from there created the islands of
Japan. Appearance-wise, Palkia is likely based after a European dragon
combined with a pearl. Its appearance may also be derived from the
Plateosaurus or other bipedal dinosaurs such as Oviraptor or
Gigantoraptor due to its head crest and reminiscent body form. The
presence of fins in their back, the fish-like head and the pearls are
possibly the reason for its Water type. Its secondary typing may also
originate from the weightlessness one experiences in water, such as
the fact that astronauts use water to train for space expeditions.

-Bulbapedia

Dialga:

Dialga, along with Palkia, may be based on the Shinto legend of
Izanami and Izanagi, who are said to have created one island with a
spear, erected a pillar on it, and from there created the islands of
Japan. Appearance-wise, Dialga seems to be based on short-necked
sauropod dinosaurs such as Cameosaurus or Brachytrachelopan while its
head is reminiscent of H. R. Giger's Xenomorph, an extraterrestrial
species that is the primary antagonist in the Alien franchise. Its
type is Steel possibly due to the hardness of diamonds, or the fact
that most parts of a clock are made of metal, such as the gears. Its
turquoise pattern on its body is vaguely reminiscent to clock hands,
interestingly, the ends of the "clock hands" are diamond-shaped.

-Bulbapedia

Giratina:

Giratina is possibly based on a basilisk. In the Altered Forme, the
wings may be based on a bat's, and its body has an insect-like,
six-legged feature, but its posture is similar to a sauropod. Its
Origin Forme has a body similar to a serpent, while the six
protrusions on its body may be based on a scorpion's stinger. However
this Forme also shares physical traits with the Amphitere, a European
dragon-like creature with wings but no legs.

-Bulbapedia

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–1 vote

No one knows the origin of Pokemon...thats the mystery of them. They weren't just summoned into existence.

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–2 votes

They definitely are NOT based off of Izanagi and Izanami since that leaves no space for Giratina. The most correct assumption so far is that they are are the 3 forms of matter. Solid(steel) , Liquid(water) Gas(ghost) from the secondary types besides the dragon.

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The spear and pillar thing seems too on the nose for that to just be a coincidence
They can still be based on the Izanagi and Izanami and the three states of matter.