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