I honestly just want a villain who doesn't even have a team. With limited resources, they simply manipulate others into achieving their goals without others even noticing it. Lust for power, revenge or boredom seem like good motives. When the player and their friends are most weak, he steps in, the person you'd LEAST expect and totally fucks you over.
Bonus props if they say they don't know how to train Pokemon but are actually really powerful.