Let me explain:
Arceus is God. And it says on some places that Mew was the 1st Pokemon so Arceus most likely made it first. And I think Arceus then created Ho-Oh and gave it the job to create the skies, and created Lugia and gave it the job of making the seas. Then Ho-Oh created Suicune, Entei, and Raikou to protect people, and Lugia created Articuno, Zapdos, and Moltres to protect the skies. Then Arceus made Kyogre and Groudon just to be guardians or whatever of the oceans and continents, respectively. Then maybe Kyogre and Groudon got into a fight so Arceus created Rayqwaza and gave it the job of stopping them from fighting and watching over them. Also I believe Arceus created Dialga and Palkia and gave them the job of creating/protecting time and space, respectively. Then Arceus made Giratina and gave it its own dimension to be god of or whatever. Groudon is the Continent Pokemon, but I bet he was all like "God, I made these continents, now what do I do??" So Arceus was like, "Okay, I create someone to help you" so Arceus created Regigigas and gave it the job of pulling the continents together. Eventually Arceus gave Regigigas its own little team (the Regis). And as we see in some of the games, there's more than one Regi team so they were all probably given the job to protect spiritual caves (I think they even say that in the anime). Then Arceus then made the Unova Musketeer trio and gave them their own jobs (Id remember what their roles are) and whatever. I think it created things such as Celebi, Manaphy, the DNA that'd eventually become Deoxys, Jirachi for the hell of it.
Okay, that's all I got. Idk if this is only a theory or if some of this is actually proven and stated. So what I want to ask is, how are the legendaries that I didn't mention (Idk if Mythical's should be included) should be included and related to this theory. For example, I don't know how Cresselia and Darkrai fits in here. Does this make any sense to you? If you need extra explaining, plz comment. I'm not sure if there's a definite answer or not. I just want to know if the relations between Legendaries have actually been stated or proven. Also tell me what you think of what I thought in the paragraph.
bonus question(?) : Are Manaphy and Phione related in terms of this case? If so, then how? I just don't get how you can get a Phione when breeding Manaphy.