Let's go down the list.
Teams Aqua and Magma are pretty much a big joke. They're a bunch of radical environmentalists with no sense of reality. Honestly people, it doesn't take a Rocket Scientist (see what I dd there) to know that if you turn the planet into either a barren wasteland or a waterworld that it would cause the extinction of almost all living beings. Archie and Maxie were morons and their Admins and Grunts were fools for following them.
Team Galactic seemed threatening at first, but Cyrus just wound up being an self righteous, egotistical, lunatic who didn't actually think his plan through. Say he succeeded in destroying the world and remaking it in his ideal image. How are you going to rule? more so, how do you and your small band of followers expect to survive and thrive? You've basically wiped out every skilled professional from the face of the earth and there would be no real order or infrastructure. I reason that it would be a pain in the ass to get anything done. Cyrus would seem incompetent, there would be discord and later anarchy. Eventually, they would all just die off anyway.
Team Plasma under Ghetsis is probably the second most evil organization. Ghetsis had manipulated a child and made him the figure-head of a group of people who thought they were doing the right thing. He also nearly succeeded his goal. The problem lies again with Ghetsis' short sightedness. What happens after you become the most powerful person in Unova? My guess is that he'd probably end up like Scar in Lion King; a bored, egotistical douchebag.
Team Flare pretty much fall under the same bracket as those previously mentioned.
Team Rocket under Giovanni is the most evil and effective team in Pokemon for the following reasons:
1. Giovanni. He is intelligent, ruthless, powerful; he's the badass amongst evil bosses and he keeps everything together. He's the Pokemon version of Michael Corleone.
2. They are smart. Instead of having the convoluted and cliched plan to destroy the world, the hierarchy of Team Rocket knows that true power lies in controlling the socioeconomic system of a country. They essentially control the socioeconomic hub of Kanto, Celedon City, thereby controlling Kanto's economy and stability and by extension, its' populace. Added to that, Giovanni has placed himself in the inner circle of Kanto's state authority. He's a Gym Leader, an essential part of the Pokemon League thereby putting him in the know and a couple of steps ahead of the law enforcement looking to stop Team Rocket.
3. They have a realistic endgame that they actually succeed in; making a profit. As I've said, they control the economy of Kanto. They also have a monopoly in the market for rare and valuable items. The illegality and cruelty surrounding how they obtain these items make them even more valuable and that makes Team Rocket even more wealthy.
4. The Grunts. the Grunts of every other team are essentially misguided fools. Rocket Grunts, on the other hand, exemplify what is means to be the most evil and despicable beings on the planet. They do evil; steal other trainers Pokemon, mutilate Slopokes, kill Cubones for their skulls and a slew of other deeds all in the name of profit and power. As if that wasn't bad enough, they also admit to their evil deeds and take pleasure in them.
