Team Rocket was the mafia. Galactic was run by a maniac who wanted to destroy the world, and Plasma's leader was basically a cult leader who manipulated people into furthering his plan for world domination.
The only suspect one is Plasma, because the grunts honestly thought they were doing the right thing. But since when do we care what grunts think?
You know, Giovanni's Team Rocket wasn't that evil (in fact, they were more akin to a local mafia, and they were terrible at it).
So far, Team Plasma 2.0 seems like it's the most "evil" one of them all, given that their members also knew *exactly* what they were doing (you can't go wrong with actively freezing an entire city, and using a Pokemon to freeze anyone to death, even children).
"Many of you feel bad for this lamp...That is because you're crazy. It has no feelings! And the new one is much better." (IKEA's Lamp commercial)