Because of the Anime people have a notion in their heads that all Pokemon are basically good, even the ones that seem to be designed to look like The Devil or Demons. They can be chaotic and destructive at time but always inevitably calmed down, and the big fights the Legendies often have with each other are always misunderstandings.
But that isn't always how it is in the Games, the Games can be pretty dark beneath the surface. And I've come to notice lately a lot of Lovecraftian influence.
Because of his status as a Creator Deity, Arceus tends to get refereed to as the God, in a Monotheistic Judeo-Christian sense, of the Pokemon world. And thus comparable to Eru Iluvatar. But while he's a creator of sorts he's not outside space and time, he's still a Finite being rather then Infinite. So at best more like a Platonic or Gnostic Demiurge.
In fact he is described as falling asleep right after creating the world. Making him a lot like Lovecraft's Azathoth. Who was in turn molded after Lord Dunsany's Mana-Yood-Shushai from The Gods of Pegena.
Meanwhile Giratina who was banished into the Distortion dimension outside our tangible universe, is a lot like Yog-Sothoth. While Dialga and Palkia rule Time and Space.
While the Fourth Generation Legendary Pokemon may be the Outer Gods, the Third Generation ones seem like the Great Old Ones. Groudon and Kyogre are primordial beasts of the Earth and Sea constantly at war with each other. They have been dormant for eons and their awakening would likely destroy all life on the Planet.
Regardless of how destructive their awakening would be Team Magma is obsessed with awakening Groudon and Team Aqua is obsessed with awakening Kyogre. They aren't Pokemon Mafia like Team Rocket or Pokemon P.E.T.A. like Team Plasma, they are cults very much like Lovecraftian cults.
Rayquazza however, who is supposed to live in the Ozone layer, possibly serves the role of Nodens, he alone is able to stop the conflict between Groudon and Kyogre. However unlike Nodens he doesn't seem like Odin or Orome, he is a very primal force of nature himself.
One could also be suspicious of Deoxys, an Alien Virus from the depths of Space. I've often felt inclined to compare Deoxys to Jenova of Final Fantasy VII.
So really a Nyarlathotep figure is all the Pokemon universe lacks.
And then if you decide to consider the Glitch Pokemon canon, all bets are off.