All the major teams we've seen so far outside Colosseum and such have been at least partially based on organizations and groups we've come to recognize as evil in real life.
Team Rocket- Mafia, crime families (Al Capone, the Corleones)
Team Magma/Aqua- Terrorists. Extremists with a fanatical cause. (Al Qaeda, the People’s Liberation Front)
Team Galactic- Religious extremists, cult. (Fred Phelps, Heaven’s Gate)
Team ?- ?
The only real force of evil left now would be evil dictators now, really. So maybe in the next game, the evil team will take over the continent for real early in the game, and you spend most of the gameplay trying to overthrow it? Any ideas?