I say Team Plasma has to be the best "Evil Team" we've seen so far. Team Rocket, is clearly overused, and quite easy to beat in the games. But since the B/W Japanese anime, they finally have more of a plotline then "We're blasting off again..." but we'll see as the anime progresses.
Team Aqua and Team Magma, are probably the worse teams ever. Not the best design, and they seemed quite weak to me. They were obsessed with expanding Hoenn using Groudon and Kyogre.
Team Galactic was a bit loony, especially Cyrus with his "creating a new world" thing, and wanted to be god.
Despite their horrible outfits, Team Plasma has to be the best team so far. They have a much deeper plotline then the others. N, the leader, isn't power obsessed like his father Geechisu, he's just confused, and finds the right path at the end of the main story in B/W.