Team Rocket, but I'm also not a person who's played every game, and who mainly grew up with the anime and only got into the games in the past 4 years. I may have had a different opinion if I played through more of the games!
Team Galactic. It's not just because I played Diamond and Pearl first, but also because the goal was to destroy a lot more than any of the other villains wanted to. I'd say Team Flare is second place in terms of how evil the goal was.
I liked Team Plasma, as most of their members simply wanted a better world. Then the leaders ended up using them to their own advantage. It's like certain real world movements where the average member means well, but it ends up being corrupted at the top and leads to unimaginable horror.
Even though the third generation Pokemon games are some of my least favourite, Team Galactic is definitely my favourite evil team. Cyrus is so incredibly selfish and ignorant of the consequences of his actions for the entire human race but he still goes ahead with his plans anyway. I think they are the evil team that actually achieved the most in terms of what their original goals were and they have a pretty huge part to play in the story (although I guess every evil team does).