If we say that the world of Pokémon was created by a form of power, religious or not, you are not far off. I am sure you have heard of how some battles end up creating objects instead, or how peace seems to destroy things.
Anyway, when Earth first came to being, it was only covered by water, and underneath the sea, molten magma. There was no life on Earth yet present. However, in space, legendary battles between Pokémon that would never again be seen or walk this good Earth, clashed and fought in the Great War of Creation. It is my firm belief that it is fought by a Pokémon of the being of Light, or Holiness and a Pokémon of Darkness, Evil.
Darkness wanted to destroy the Earth, for it hated all forms of beauty and was able to foresee the beings of Pokémon forming on Earth, and later by the race of Men. Light however, wanted to preserve this place as a form of paradise, for it was curious, how a separate specie from its own, would govern this Earth, filled by water.
Thus, the Great War of Creation was fought, when Light raised mountains, Darkness sent them back into the sea. When Light grew forests, Darkness burnt them and engulfed them in flames. When Light attempted to create beings, Darkness would smite at it, ruining all of his efforts.
Finally, Light decided that it would no longer put up with Darkness's secret war against it any longer. Light put forth of all of its strength to attempt to banish Darkness from this Universe. However, Light and Darkness are extremes; one cannot co-exist without the other. Therefore, before retreating into another Universe with Darkness to continue a seemingly endless fight, it created an Egg, the first in time, and left it in Space, protected by an Aura as long as Light still lives on.
Thousands of years later, the Egg hatched into a handsome Pokémon, which we would later revere as Arceus. In Arceus's mind alike, as like it's creator, was to create life and start a revolutionary existence of co-existence of creatures. However, Arceus had great wisdom and believed that it could not do this alone. Thus, from part of its power, it created the Trio, Diagla, Palkia, and Giratina, giving it one of its abilities, control over Time, Space and Anti-matter respectively.
However, Giratina, although destructive by nature, is actually created by Arceus as a form of balance between the extremes; Arceus was creative by nature, yet Giratina was destructive. Thus, Giratina was sent to the Alternate dimension, or the Distortion World, where it could create a balanced world of destruction, or nothingness. Thus, when people say when something completely vanishes, it goes into non-being, which is to say nothingness, they are not far off.
However, Diagla's responsibilities was the heaviest, as it was responsible for the ageing of things and time. It is not wrong to say that time is a being itself as it too, has an age. Yet, there were no creatures in being at that time, therefore, the only thing that was ageing was time. However, the Trio, and Arceus, were immortal, and would only pass into non-being if Light was to perish in the Other Universe. Creatures able to time travel are only Arceus, Diagla and Celebi(It is unclear why Celebi has the ability to travel through time).
Palkia, however, Space is designated as a form of what we call, fate. This Space is controls what we all do, where our "future" would take us. Therefore, the theory of everyone in the world being linked together is not a totally incorrect theory, as its link is Palkia, but this link few can see, the only ones known to be able to this would be Arceus and Palkia themselves. However, if this link is to cease, Men and Pokémon alike would function independently without the need of someone else, or putting trust in each other. But the rationale of the creation of creatures are for them to co-exist in harmony. Thus, Arceus created the Lake Guardians, Uxie, Mesprit, Azelf, and bestowed upon them knowledge, emotion and willpower. These Lake Guardians would help Palkia create the foundations of all beings, for even the most un-feeling people would have emotions. The most foolish people would still have knowledge. The most weak minded people still able to rally themselves if need be.
Soon, Kyogre and Groudon fought their legendary battle among each other. In this battle, when Groudon spat molten magma at Kyogre, Kyogre solidified it, forming new grounds. When Kyogre assaults Groudon's territory, it floods them, creating new water territories.
At this time, the battle which the legendary Arceus had purposely allowed, Rayquaza was given the go-ahead by the trio to quell this battle, as the new lands were to their liking.
So, from the fortress of Sky Pillar, Rayquaza descended on the two, and forced them to hide in its wrath. Following its duty, Palkia created the Red and Blue Orbs, to prevent them from engaging in battle. Palkia set these orbs on Mount. Pyre, and with the help of the Lake Guardians, embedded into the minds of the creatures there, later created, the old knowledge of the true meaning of the Red and Blue orbs, the pride to defend it, and the will to defend these orbs to the very last.
It is unknown that who created Mew, the first creature to walk Earth, but it was believed that they existed in great numbers at that time. Could it be that they were test subjects for this Earth?
Anyway, when other Pokémon started to appear, such as Kabuto, their numbers swiftly declined, such that only one was left in the entire world. To this Mew, Diagla and Palkia granted it immortality.
Then, the Regis were created by Regigigas. It is of a lesser post in the duty of world creation, but nonetheless, shaped continents with different elements.
Men raised the Brass Tower and Tin Tower where Lugia, the Guardian of the Seas and Ho-Oh, the Guardian of the Skies repectively, in of worship the Seven Seas and the Holy Atmosphere. When a bolt of lightning sturck the Brass Tower and set it ablaze, three Pokémon were killed, and Lugia fled the Brass Tower and sought refuge in the deep sea trenches of Whirl Island. Ho-Oh left in search of a pure-hearted trainer but came back to revive the three Pokémon that perished in the blaze. This proves that Ho-Oh has control over the creation of life and have powers of bringing back the dead. The revived Pokémon are Suicune, Raikou and Entei, whose types represent the event that killed them. Raikou represented the lightning that started the fire, Entei, the blaze, and Suicune the rain that doused the inferno.
Therefore, the Three Pokémon mentioned above, are of a "lesser" being, but still wields deadly prowess in the field.
Then, as a last act, Arceus relocated The Lake Guardians, away from what would later become cities and towns, away from humans, for Arceus foresaw, that the Race of Men desired knowledge, fame, power and above all else, were greedy than other creatures. Yet, it knew that they were to be the pushing force of Earth, therefore, the Trio and the Lake Guardians, created Men together, and the Trio would return to their own dimensions, Arceus into a deep slumber, and the Lake Guardians dwelt in their lakes, waiting for a call from Arceus, to readily end or start a life.
Meanwhile, the Race of Men have advanced through the ages and have reckoned itself to be the ruler of Earth, giving no heed to superior beings like Arceus.
However, in certain locations, Pokémon was revered, such as the Shrine dedicated to the Guardian of the Forest, Celebi, or towers which was built for Lugia or Ho-Oh, unique Pokémon which were created by the Lesser Gods to help manage the huge populations created, and different "legendaries" were given their own powers over others, for example, Lugia over the Three Birds, Zapdos,Moltres and Articuno.
Meanwhile, recent events have proven the wisdom of Arceus, with Team Magma(Aqua) and other organizations seeking to awake Groudon(Kyogre), with Rayquaza still dwelling in Sky Tower.
Also, against the will of the Trio, Men have tried to play the role of Arceus, such as creating Porygon, or Mewtwo, a gross genetical splinch of the original Mew left in the world.
Pokémon have also become slaves to the Race of Men with their advances, the Dark Ball, for example, enslaves the Pokémon to the owner's will completely, and makes it evil, while enhancing its abilities significantly. Although the general community have banned the use of the ball, a decent amount can still be bought in the BlackMarket.
Yet, there are Men who are also influential members of the society, who wants to resurrect the idea of Arceus, co-existing with Pokémon instead of tools for trade. Yet, that also included space exploration to look for Arceus, like Porygon2, though their search will be futile, would raise hopes of a better Pokémon world, with Arceus's ideology in mind.