But may I ask why you dont think God will be on the 3rd version?
First things first, Arceus is not "God", not in the Judeo-Christian sense. Not that you're the first to make this mistake nor will you be the last, but just the same. Pokémon draws most of its cues from eastern religions, particularly Shintoism. The Shinto concept of deities differs greatly from the Judeo-Christian concept of "God", a single, all-powerful, all-knowing entity. Shinto deities - "kami" - are divine to varying degrees and revered as such, but the concept and the reverence of these kami are very different from worship in the Western sense. Because the comparative religion class is two floors up and three doors over, you can read more
here.
Second, because it won't be. That simple. Arceus is an event Pokémon and not only will they not include an event Pokémon in a core title without some stipulation, like an event or forcing you to transfer it over from a side title like Ranger, but they certainly would not stick such a critter on the box art. It just doesn't work that way. The caretakers of the franchise go to great lengths to manufacture artificial scarcity for certain Pokémon and there is nothing to be gained by chucking that scarcity out the window for no reason.
Hopefully this can lay this issue to rest.
But he IS God, He created everything and was born from a beam of light that formed an egg that contained the "Original one" and Giratina is the Devil. Just speculation but it could be true.
No, as we've just established, Arceus is not "God", nor is Giratina "the devil".
What about the ??? typed Arceus? could be possible No?
No. For all intents and purposes, the ???-type Arceus does not exist. It's in the code only as an utmost necessity and will never, ever arise in any sort of legitimate situation, gameplay or otherwise.
I'm not saying they have to top Arceus, but that just seems the basic standard for the legendaries, and it is usually brought up by other users.
That last bit says it all. Much like the concept of Arceus being God in the western sense, the "need" to top Arceus exists only in the mind of fans.
And I considered the 'religious' idea since there has always been scientific and religious themes in Pokemon, so the afterlife pokemon might not seem all that farfetched.
No, it's as farfetched as can be. Pokémon is as much an international franchise as can be in the modern day and as such, Game Freak knows full well to stay far, far away from religious matters or anything of the sort, to avoid any kerfuffle during international releases, and if they don't know that on their own, I'm sure Nintendo of Japan makes very sure they are made aware.
The only time they've ever come close (Arceus), Western fans misinterpreted the concept severely, making it out to be something it very much was not; see above for that explanation.