Giovanni - Pokemon for profit (mob style)
Archie/Maxie - weather plan that wasn't thought through but cutest admins in the series
Cyrus - Going to rebuild the universe in his image as a god the absolute madman
Ghetsis - Gendo level parenting skills with an unrealistic plan of being the only person in the world who would own pokemon.
Lysander - Too many corrupt people using the regions resources. Better kill everyone except the most corrupt people and start over.
Out of them I would say that Giovanni had the best overall organization. Cyrus though gets the best outright Evil Leader award, who just says fuck it to everyone. Archie and Maxie I almost don't count as evil teams because of how they didn't really have any malice in their goal, but were so dumb in their planing skills.