My main goal would be to bombard Unova with missiles. When the player faces me the scene would start with me clicking the release button and a counter counting down from 600. They need to approach and win me or they fail. [insert evil laugh]
Gamefreak better add a feature that can topple this fairy type.
Splice together Pokemon DNA to create Pokemon Fusion, and give them better stats at the same time, eventually creating the ultimate Pokemon, capable of learning every move with base stats better than any Pokemon in every category.
Create an army to forcefully control the region/world.
Breeders would raise standardized pokemon, constituting different branches of the army, namely Skarmory, Aron, and Piplup. Durant, Bronzor and Magnemite would be issued out by request for the soldier's preference.
Recruitment would be hush-hush style until strong enough to take over a major institute or small town. Once complete, the team would work with the townsfolk or whoever runs the major institute occupied to further successes and/or improve living conditions. Then it's open recruitment and standardized training as well.
Ground forces train for double battles, air forces learn Fly, and aquatic forces have the longest training period to get their Piplup to evolve into Empoleon. Each branch trains to operate alongside each other.
I guess this kinda storyline would be about a revolution that frees pokemon from this kinda life and forced responsibility. The player would have to deal with an evolving political landscape and hostility from both radical revolutionaries and my team's soldiers.
What's the point of living if we're all just born to die?