I have not played Sun & Moon, though I will say that Team Skull's theme is one of the top villain themes.
Team Rocket = Team Galactic > Team Plasma > Team Magma/Aqua > Team Flare
Team Rocket's classic bad guys and I'm a sucker for the Yakuza/Mafia archtype. Additionally, Giovanni has plenty of different takes, but I particularly like the game's implication that he actually does think highly of his troops.
Otherwise Team Galactic is very well-rounded, even if they have the most fantastical plot.
Magma/Aqua rank higher if counting the remakes, but lower without them.
I haven't played Black 2/White 2 so I never really got to see Colress in action. in Black and White, Plasma's themes are explored well, but only N and Ghetsis are really worth anything.
Everyone knows the issue with Team Flare, but I'll just go ahead and say that I cannot remember anyone except Lysandre, Xerosic and Malva, and I'm sure I'm not the only one.