It will be based in a new region where there is a scarcity of pokemon, but an abundance of Z-Crystals and mega stones relative to the other regions.
Background: new region is discovered, and adventurers discover the crystals and stones. This results in a mass flood of immigrants looking to get rich quick (similar to the California Gold Rush). After a hundred years or so, these immigrants form two sides- East and West. The West side begins running low on Z-Crystals to sell, but the East hasn't; however, the West has far more efficient mining processes due to the terrain in the West and other resources. As a result, the West has more crystals and mega stones for stronger military power. The West creates deals with the other regions (Kanto, Johto, Sinnoh, etc) promising them cheap crystals and mega stones in return for soldiers (aka trainers with pokemon). So the East side has an extremely uphill battle.
How war is fought: trench warfare modified to pokemon. Basically soldiers mobilize through the trenches, but also support and cleric pokemon (grass, poison types) reside there. Steel, rock, and ground types form a wall in front of trenches, so the clerics heal them as they fight while the clerics can't be hit. to push trenches, each side uses 1 of 2 strategies (or both at the same time i guess):
-Rush with grass, water, and ground z-crystals to take out the walls
-"smoke" the clerics out with poison (gas), fire (smoke), and flying (wind) z-crystals
Story: The main character (who's backstory is cool imo) is caught in the middle of this war, and of course, is on the East side cause they are automatically the good guys cause they are weaker lol. His ace pokemon, Dhelmise, puts him in a peculiar situation.