Team Rocket is iconic, but at the end of the day they're merely a generic crime syndicate. Team Rainbow Rocket does add some flavor to it but at the end of the day, for all they achieved, that's all I see them as. There is something to be said for that simplicity and sort of realism though, so it's not all bad.
Team Aqua had great outfits and I can see where Archie is coming from when he explains his goal in Alpha Sapphire. Not a bad team overall.
Team Magma doesn't have as much of my sympathy as Team Aqua. An all right team, but I don't like them as much. Maybe that's better in a way, they're actually a higher degree of villain to me, but they lack the fashion sense and character in comparison.
My apathy toward Diamond/Pearl/Platinum extends to Team Galactic as well. Cyrus' goal is neat and all, but I'm just left exactly as he wanted us all to be, bereft of emotion. Probably my least favorite villain team overall.
Team Plasma is pretty good. Ghetsis is great at being a monster, N has his redemption, and the Seven Sages, Anthea, Concordia, and the Shadow Triad are nice little touches of spice. Their goal isn't too bad. The castle raising up behind the Pok?mon League was great. The grunts' knightly outfits are pretty cool and Ghetsis' robe is nice. It was also nice to be able to hunt down the Seven Sages in the postgame of Black and White for Looker, and they're responsible for the creation of the current form of what we know now to be Genesect. Overall very solid team for me.
Team Neo-Plasma is okay I suppose and Colress is all right. I liked that there was still a faction of the original Team Plasma who stayed loyal to N including Anthea, Concordia, and former Seven Sages member Rood. Ghetsis' increased depravity and jacket are pretty nice to see too.
Lysandre had the plan which I most sympathized with, but the rest of Team Flare was underwhelming and they aren't really anywhere near the top of my favorite villain teams.
Team Skull are great and I love a ton about them. Their designs look nice, their dialogue is enjoyable, their battle music is fantastic, I love the look of Po Town and their base in Shady House, the abandoned mansion in Po Town. And of course they're lead by your boy Guzma. What's not to love?
Aether Foundation is pretty cool. I don't really have much else to say about it.
I'd probably rank them as follows:
Team Aqua > Team Skull > Team Plasma > Team Rocket > Aether Foundation > Team Flare > Team Magma > Team Galactic
It was tough to decide whether to put Team Aqua or Team Plasma in 1st Place. I gave it to Team Aqua for Archie's stated motivations being more interesting, despite Team Plasma having more substance and flavor with all of the NPCs in their ranks. Team Skull landed between the two for 2nd Place because they're just so lovable. I feel like my preference between Aqua and Plasma can switch depending on the day though.
If we were talking about the bosses based on their own personal objectives, then:
Lysandre > Archie > Lusamine = Guzma (I refused to put him lower than the rest) > Maxie > Cyrus > Giovanni > Ghetsis (lowest in this ranking because he just wanted to be the only person with Pok?mon and to rule, boring)