Pokemon is life.

There are a few points I'm impressed with, and some that I'm going to disagree with.

Arceus and Giratina: I kind of disagree with Arceus being a representation of monotheistic god, and I totally disagree with Giratina being Satan. Satan (supposedly) does two things: punish evildoers and promote learning. How does Giratina do either of those things? Rather, I would group him more closely with Palkia and Dialga. Where those two have absolute control over time or space, Giratina has limited/corrupted dominion of both. He's incomplete, as evidenced by the broken nature of his realm, where waterfalls flow up and sequence seems to mean nothing. Not evil, just broken.

5 Legendary birds: I like where you're going with this, but I think something can be improved. Ho-oh isn't my favorite, but I do like its elevated status here. Lugia, Articuno, and Zapdos can be interpreted as forms of precipitation (or accompanying weather effects), with Moltres being an oddball as a not-precipitation weather effect. Shouldn't Lugia be the special one instead? I can't think of a way to put these pieces all together better than you have though, so I would just break it apart as Kantobirds being the three basic elements of JRPGs (which, honestly, is probably their origin. Just go here and click "open all folders" then scroll down really fast. Pokémon is not unique in making a set of these three elements), and leaving Ho-oh and Lugia as the sun and (full) moon.

Regi: Wow. I never thought of it as that, I was instead thinking of how the first three are each solid components of the planet: glaciers+icecaps, bedrock, and the molten metal core. But the sequence of technological ages? I like it. Not entirely historically accurate unless we mix Bronze, Iron, and Industrial ages all together for Registeel (which still works in historical order), but I think it's pretty solid, especially with Regigigas' reasoning as the computer age. Now I just want to see a space age...

Darkrai and Shaymin: I'm sorry, but what? Okay, maybe with some suspension of disbelief, but it seems like you're forcing them together. They work just fine as perfectly separate entities who just happen to contrast with one being creepy and the other being cute. Compare it to Cresselia and Jirachi combined, who are even farther from each other in the Pokédex, their combined explanation makes more sense. At least if Jirachi is one special star (a wishing/falling star, perhaps), as an explanation for why there's not trillions of Jirachi and only one Cresselia. I do like that one though.

Three beasts of Johto: Wut? How do Suicune and friends have anything to do with any geopolitical entities of the world? Like, at all. I like the Burned Tower idea better: Lightning struck the tower, it caught fire, and rain put it out. All three were there, that's why you find them in the basement of that building. If anyone can justify this Avatar-esque reasoning for the three beasts, I'll give you a like and a donation of 100 pokepoints.

Mew and Mewtwo: Regular life and life augmented by humans/science? I like it, I really do. I want to do a similar thing with Gensect, but need to find his Mew first.

Zygarde: Here's something I just thought up with your help: Zygarde is a serpent, so how about we make him the circle of life when he takes the form of an Oroborus? It contrasts a little with the news about Pokémon Z and its inclusion of the various percentages of Zygarde, but a serpent, circle, oroborus, and self-consumption? I like the idea of him representing the circle of life.