I am at a loss. I'm torn between the insane Team Galactic, and the efficient Team Rocket. I'm going to have to go for Team Rocket for a few reasons.
1. Giovanni: He is a badass, no doubt about it. No matter where he is, anime, game, manga... anywhere. He always has an air of power surrounding him that makes you nervous. His pokemon are some intimidating creatures, too. Nidoking, Nidoqueen, Rhydon, and Honchkrow. If I were Gold, I'd be pretty intimidated by Giovanni's choice of pokemon.
2. Deeds: Team Rocket is the first, and only team to actually take control over two cities in a region. Celadon and Saffron. They controlled the Casino, which is probably one of the biggest places in the city, and they run Celadon from there, since its members could walk around without fear. And in Saffron, they blocked off everything, and basically took over the town.
Then there is them mutilating pokemon to earn them money. Cutting off Slowpoke tails, prematurely evolving pokemon, which probably causes them a lot of harm due to underdevelopment. Then they outright murder pokemon, judging by what happened to Marowak.
3: Longevity: They went through three, count them, three regions. (Kanto, Sevii, Johto) Before they were squashed. Kanto, Giovanni did indeed disband them, but under Archer, they come back in Sevii, and later on Johto. And even after Archer leaves, a Rocket who speaks like Yoda, keeps Team Rocket alive in Kanto, nearly destroying that country's power supply.
4. How good they are at what they do: Team Rocket has a lot of confidence in their ability so that they blab about their plans. However, they always nearly succeed, despite the fact that they ruin everything. If Team Rocket didn't blab, then there would be no way they would have lost.
5. The size of it: Especially in the anime! Team Rocket is, arguably the largest organization of all of them. To have enough members to seize an entire metropolitan city that is probably as large as something like Phoenix or Dallas, and to post members to take control over an entire building quite throughly. (Note that, while it isn't in any of the games, taking into account that this is supposed to be the equivalent of a successful nation, and Saffron is the largest city, so in real life, it'd probably be about that big)
6. The Team Itself: It's a terrorist mafia that takes advantage of trainers, sells drugs, runs a casino, steals pokemon, steals items, steals money, threatens murder, murders pokemon, takes over a city, and holds the Gym Leader, the Dojo Master, the police, the Silph Co, which is widely regarded as being one of the most powerful companies in the world hostage, creates many clones of creatures and humans, experiments with pokemon, sabotages a power plant that supplies power to an entire nation, causing it to descend into chaos, takes over another city, holds another gym leader, a media director, and the largest city in the Kanto-Johto region area over. That's not including Pokemon smuggling, kidnapping, identity theft, pokemon mutilation, torture, and exploitation. And then we have them in Sevii, where they pretty much try to kill off an endangered pokemon, and an Elite Four member.
Damn. And that's not everything, either. It's most of it, but not everything.
7: The outcome of their goals: All they want is money and slave pokemon. You see all of the stuff that was up there? All of that horrible, horrible stuff that they did? They did that for only money. For just money, they did all of that horrible stuff.
Those are the seven reasons for my like of Team Rocket over every other evil team. Team Galactic is a close second, though, Team Magma is third, and Team Aqua is last, but I like all four.
But my favorite team, including spinoffs, would be Cipher, but I don't want to write another list, so yeah.
