I'd steal Pokemon, make money, maybe genetically enhance a cat, give all my employees Rattata and Zubat, and rub my hands evilly. --- I'm not easily impressed; I'm usually oblivious to whatever's in front of me.
The classic Team Rocket motive. Get tons of money by using and stealing rare and powerful pokemon. --- "How the Christ do you expect to reverse-Atlantis an entire city? You're just the Dragonborn, not the Daedric Prince of Civil Engineering." - DocWily
Get all the Japanese Female Pop Idols ages 16-25 to serve me as their master and one only love by sending subliminal messages via radio antennae using Jiglypuff, Hyprno and Rotom. --- "imagine if Metallica got together with the Power Rangers and the coolest kids in school and had a party in your mouth, and you were invited" THE_WIND
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. --- Excuse me, sir? Can you sign my bus schedule?
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?
Take down the other evil organizations, though evil means. i.e. torture, poison, etc.
In other words, it'd be an anti-hero organization. (for those who don't know, an anti-hero is a character who achieves the greater good through evil means.) --- 4e is not D&D, but WoW making a Disguise check. Pokemon Black Friend Code: 0605-2800-9952; Trainer Name: Solace; First Pokemon (roleplaying): Shiny Umbreon