I'm totally sure this isn't possible, but we need a dark, rocky plain shrouded by thundering clouds as the final destination. It can be the connecting point of the regions, where Pokemon truly began, the reason behind the powers of the legendary Pokemon. It all centers there.
If someone could picture that solemn scene and slightly edit a similar scene somewhere in the Pokeverse, that would kick butt. It would help with story development so much.

which one?

Funny.
Just one of them.

There was a scene sort of like that in a Pokemon game:

Spoiler:

Pokemon Mystery Dungeon: Explorers. You and your partner scale the Temporal Tower, in order to reach the very top. Despite how high up you are, there are dark red storm clouds looming overhead. There, you find what you've been searching for: a stone tablet with holes in it for the five Time Gears. (Background information: The five Time Gears are from specific areas in the game. When you take a Time Gear from an area, time stops there, but if all five Time Gears are not placed in the tablet, Temporal Tower will crumble and collapse, and time will stop everywhere, turning the world into a terrible wasteland.) You and your partner don't see anyone else around, so you make a mad dash for the tablet, when suddenly, there is a bright flash of light, and standing before you is Dialga. Your partner attempts to reason with him, but he will not listen. Temporal Tower's decay has caused Dialga to revert into his Primal state, and you realize there's no getting around him. Needless to say, you must defeat Primal Dialga and save the world before it is all too late.

I'd like to help imagine this place, but first I'd like to know what exactly is supposed to happen there.

Oh, yeah. I played that game. It took a few times, but I kicked Dialga's butt eventually.
Something like that, except not like a building.
The place I desire is where Pokemon all started. Pokemon have always had strange powers, like Celebi's power to travel through time. Even Acreus, the so-called god of the Pokemon, doesn't fully explain how the amazing Pokemon became so powerful. And this cloud-shrouded, rock-covered plain is the birthplace of the Pokemon, all of those millions of years ago. Something happened here, something no one bothered to investigate or even question. Until the leader of the evil organization happened upon it. If he could discover what became the first wave of modern Pokemon, he could easily create the ultimate Pokemon at the source.
You see where I'm getting at?

Precisely. You want to imagine a "spot of creation" where Arceus landed on Earth and created the first Pokemon.

Well, currently what I'm imagining is a congregation of all five of the major villains (Giovanni, Cyrus, Ghetsis, etc.) working together to capture legendary Pokemon, bringing them to that specific location, and attempting to decipher what exactly is the source of their strength. Pokemon that could play a role in this are:

Spoiler:
	- Victini - Celebi - Jirachi - Mew - Palkia - Dialga - Darkrai - Manaphy - Legendary Birds - Legendary Beasts + Unown - Lugia/Ho-Oh - Latios/Latias - Legendary Earthmakers (Groudon, Kyogre, Rayquaza) - Deoxys - Legendary Guardians - ...Regigigas? Shaymin? Anyway, you get the idea, any legendary Pokemon with an excessively powerful or dumbfounding ability.

Now, if we wanted to do something really awesome, the best thing we could do would to be have the villains combine their own evil intentions and all the different legendary energies to create a new evil Pokemon to be their tool for conquering the world.
Of course, we would have to imagine this ourselves. Essentially, it'd be like the Pokemon equivalent of the Devil, 'Dex number of 666 and everything. The conclusion of the game would show a cutscene with the villains and the captive legendaries off to the side, and we watch the Poke-Devil defeat Arceus in battle. The villains notice you, and command the Poke-Devil to attack you. How the fight would work is arguable, but I think this would be a pretty awesome conclusion.

Except that it would also require an origin story for Arceus instead of saying he always existed. Doesn't he have some jewel in his head? Maybe we can make that the origin of his power. That's why he can change types. Or something like that. I'll come up with an elaborate story, just you wait.

Well, let's take a look at Arceus' Pokedex descriptions.

"It is said to have emerged from an egg in a place where there was nothing, then shaped the world."
"It is described in mythology as the Pokémon that shaped the universe with its 1,000 arms."
"It is told in mythology that this Pokémon was born before the universe even existed."
"According to the legends of Sinnoh, this Pokémon emerged from an egg and shaped all there is in this world."
So all of these seem to have the same basic theme. Arceus hatched from a single egg, and created everything else around him from there. Mysteriously.
So, however he did it, Arceus invented all locations, all Pokemon--and, by extension, all types. We also know that if Arceus is holding a Plate item, their type changes to the type respective to the Plate.
Logical conclusion: Arceus crafted several hundred of these mysterious Plates (through whatever his power is), and weaved them into a Pokemon's essence to give them their unique type. But Arceus did not want to be binded so--they did not place a Plate within himself, and therefore could become every type.

But anyway, about Arceus' powers' origin, there appears to be another Mystery Dungeon game coming up that will brush upon this topic. If you can't think of anything, perhaps we should wait it out and see what this game comes up with?

Also, a thought about the Poke-Devil: Since Arceus can be every type, I think it'd be interesting if they had no type (The way Shadow Rush dealt no specific kind of damage). This would mean they can learn every type of move at once. If they have to have weaknesses, they could be based off of the move they used last.


Lastly, that face is the funniest thing ever.

Woah woah, hold up.

Someone explain to me what you're all talking about here.

@CF: No, I know your making up parts of the story but Arceus is way overcredited
Arceus only created a flat earth and a few Pokémon, the Legendaries.
He made a flat earth and sent Mew to make all Pokémon, then he sent Kyogre to make the oceans and Groudon to do... what ever he did, and Entei to make volcanoes.
Then he made Dialga and Palkia to make space and time, etc.

And I know the stories about some Pokémon don't match up, like Entei was born in a volcano, but that would be insisting that he's young compared to some Pokémon, and in some situations might be younger then some fossil Pokémon.
So when you read legendaries descriptions together you see the puzzle of the Pokéverse fall together.

So you could keep the whole plates thing, just change it so Mew made them and he went to "plate" them I guess... Just don't undercredit the rest.

Well, here's what I think. Instead of A "Devil Pokemon'? We should Have the "Leaders O Evil" In A search for the Ultimate Pokemon, And so, They Build a Machine that Combines the (Arguably) Three most Powerful Pokemon. Regigigas, Defense Form Deyoxys, And Groundon.Thoughts?

How about we just have a single team that is after all the main legendaries.

Eh, Ask Silver. She's the one Who ultimately Decides, after all.