Why can't Celebi have come from the future and brought Arceus, who shaped the world. Celebi is now at the beginning of time, and Arceus creates Dialga to give it Time to roam into. Palkia is created to give Celebi a place to go.
Then, they all start to fight, and Celebi leaves, because it is no longer peaceful. Arceus creates Giratina to subdue Dialga and Palkia, but Giratina hides in another dimension. Arceus learns that the fighting will not be solved by fighting, and eventually Arceus creates Uxie, Azelf, and Mespirit, who calm down everyone. With Knowledge, Emotion, and Willpower created, the ability to Wish is born, and so Jirachi is shaped out of these emotions. Jirachi senses the empty earth, and makes it able to be populated with Pokemon. Mew is born from this wish.
Meanwhile, Arceus realizes that the Earth isnt doing much. He creates Regigigas, who tows the land into what Arceus (and Palkia, I suppose) wishes. However, the Earth is not doing much, so Arceus creates Pokemon to manage opposing weathers: Rain and Drought, with Kyogre and Groudon. However, after their epic battles, Arceus sees that the world is not as it should be, and creates Rayquaza to manage a balance between the two.
However, it would seem that not all legendaries are actually unique. Even though Mew is said to be the ancestor of all Pokemon is Diamond, in FireRed the Pokedex entry is as follows: "A Pokemon of South America that was thought to have been extinct. It is very intelligent and learns any move." This suggests that, while Mew may be the ancestor of all Pokemon, it created more Mews.
Another point would be that more than one Lugia has been spotted. This suggests that only a few Pokemon are truly unique to the world.
Also, Heatran can either be male or female.
Speaking of Heatran, according to Bulbapedia, Heatran came from the volcanos when the world was first formed, and the lava and magma pooled together to form it. That works for me.
Now, we know that after this there are many ancient Pokemon: Aerodactyl and Kabutops are just examples. However, after a while, they went extinct. Using a fallen comet as a basis for this, I suggest that most ancient Pokemon (except the legendaries, they are powerful enough to sustain themselves) died out, and from this comet came the virus that would eventually become Deoxys.
During all this nonsense, Regigigas must have walked the earth to see how it was. As it walked, bits and pieces of it eroded off of it and fell onto certain elements: Regirock spawned from a piece that landed on a mountain, Regice from a piece that fell in Antartica, and Registeel from a mix of the piece of Regigigas and the virus-free meteorite, thus creating Registeel (this would explain why the metal is unknown to the scientists).
Eventually, Lugia and Ho-oh are born: One to Guard the Seas, and one to Guard the Skies. Eventually, born from Lugia comes Latias and Latios. Ho-oh flies constantly around the sky, bringing the newly-evolving Pokemon happiness and life, but Lugia remains underwater, breeding new Flying-like Pokemon, like the aforementioned Latias and Latios. Eventually, three Birds are born: Articuno, Zapdos, and Moltres. Lugia makes sure these three stay peaceful, for it is their parent.
Around this time, Cressalia falls from the moon and establishes the fact that travel is possible from the moon. Other pokemon fall from the moon as well, such as Cleffa.
Finally, many more Pokemon start taking form. Jirachi grants a wish once more to create Shaymin, who guards mother nature and make sure she stays clean and fresh.
Also, I think that Giratina creates Darkrai to plague the world that Arceus created out of spite for Arceus. That's all I have about Darkrai.
After a while, humans show up (I don't care how, this is more about Pokemon), and humans eventually build many things, and grow vastly. They build many structures, including the Tin and Ecruteak Towers (Brass Tower). However, war eventually destroys these buildings, as well as some Pokemon inside it. Ho-oh is near at the time, and revives three Pokemon especially to be the embodiment of some sort: Raikou, the embodiment of the speed of lightning; Entei, the embodiment of the passion of magma (??); and Suicune, the embodiment of the Northern Wind.
With human research comes the ability to revive ancient Pokemon as well as create new ones. Deoxys is finally created when the viral DNA encounters a laser, and Mewtwo is created from an epic reviving maneuver.
That's my theory on it anyway. Time travel solves everything :D
Oh, and I saw a lot of people talking about plates? Well, we can say that Arceus used each plate to create a different Element, and is the physical manifestation of said element into a form that only Arceus can use, thus giving him power over all elements. However, over thousands of years, the plates got buried and such. I think that's pretty good.
