Meloetta?

Name: Final Fantasy x Pokemon: Simulation
Company: Maxis/Square Enix/Nintendo/Forgotten Hero Publishing
Genre: Simulation, with JRPG-style battles sometimes.
System: PC

Gameplay:
This is a large-scale environment simulation game, in where you use the powers of each Pokemon to help attract humans back to the destroyed regions. Think a lot like Sim City, or the simulation parts of Actraiser. During the story mode, there are also times you will roam with a party of four, to help defeat villainous Pokemon who desire to scare the humans off. At these times, it turns into a side-scrolling action game.
A lot like ActRaiser, now I think about it.
Not only do you need to fix the lands, you need to keep every Pokemon happy - if they aren't, they won't work for you, and you'll lose that skill. Every Pokemon has their own niche ability, though some are replicated. There is also Pokemon Breeding, Deoxys seems to enjoy this.
After you beat Story Mode, you can start Free Play mode, where you can summon the Villians to destroy your world, if you like.
There are also side stories, which are basically limited to a small region of the land, and locked to certain characters.
Characters:
Most of the heroes from Dissidia: Final Fantasy are present - with only five villians having been brought in. Some characters from Theatrhythm and All The Battling were brought in as other legendaries, as well.
However, they all seem to have amnesia. As the story progresses... well, that's a secret, one which Meloetta doesn't know yet. If you really need to know these spoilers (for example, if you want to join this AU), send me a message. I'd rather not reveal it to everybody. It's gonna be a tragic surprise.
Yuna is with the Unova group, and these are the only others she knows.
This group includes:
Zidane, the Mew.
Bartz, the Victini.
Rinoa, the Articuno.
Vivi, the Phione.
Environment:
This is from a version of the game with all regions - from Kanto to Unova, and the special edition Orange Islands and Orre DLC. The Pokemon can go to any region, as well! Though, they tend to keep to their own, until somebody plays to that point in the save file they come from.
In a few places, mostly in Johto, the air is toxic. Until that event is cleared, of course.