>>29550182Ghetsis > Cyrus > Giovanni > Maxie > Archie > Lysandre >>>>> Human Excrement > The worms eating the excrement >>>>> The excrement of those worms > Archer
Ghetsis is my favorite for being a pretty manipulative bastard and also stacking the deck so that you can never catch him. Even though he fails twice, he's a hair's breath away from having the Unova region twice over, obtaining two Legendaries in the process and having a third being worked on.
Cyrus was a favorite of mine for similar reasons, since Team Galactic captures four/five Legendaries depending on the game. There was also his flawed mentality and desire to create a world that he didn't even fit into.
In terms of teams, I'd say
Team Galactic > Team Plasma > Neo Team Plasma > Team Magma > Team Rocket > Team Aqua > Team Flare > Neo Team Rocket