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Okay, so... I already discussed this with a friend and I want your input, because I want to see if this is worth putting a team together.
The gameplay is a bit awkward. You have Turn Based Strategy ala Advance Wars and Fire Emblem(but with more traditional Command and Conquer gameplay ideas thrown in,) and you have regular Pokemon gameplay stuff.
The turn based strategy part of the game would be like the Strikeforce missions from Black Ops 2, making large changes to the Pokemon world. You can pick Nod or GDI, and you duke it out over cities, plains, and forests to either corrupt it all or to try to preserve as much as possible. It makes sweeping changes to the Pokemon world as you do this, and is unlocked after your first gym battle(or complete the optional prologue which doubles as a tutorial.) Despite it being more of a side thing to change how the world is to make certain things impossible in lieu of certain impossibilities becoming possible, you can technically complete the whole game through it.
The Pokemon part of things doesn't really need much of an explanation. Body part damage, a more mature story(if I can think of one that isn't just pure edge), and otherwise traditional Pokemon gameplay. As things progress with the GDI vs Nod situation though, Pokemon may undergo mutations thanks to the foreign material known as Tiberium.
The story set up we have is pretty simple. Basically, at the end of Command and Conquer Tiberian Sun, GDI gets their ass kicked in. So hard, infact, that the World Altering Missile gets launched. The (optional) prologue opens up with GDI trying to survive across 5 missions against heavy tiberium infestations and remnant Nod forces. Eventually, GDI gets a lucky break, and unlocks the power to escape into a whole new world, and Nod chases them into this new world. Unfortunately(for GDI,) GDI and Nod both track a little tiberium into the Pokemon world, beginning the crisis in a new world.
