Not really sure, to be honest. Most of the evil teams are pretty damn ridiculous plot devices, when you think about it.
I mean. Team Rocket are just straight-up Poké-Yakuza. Big, boring but effective criminial syndicate who probably have their hands in just about everything in the Kanto/Johto region and masterminded by an outwardly respectable member of the community (that said, if Viridian wasn't entirely a Mafia City, I would be immensely surprised). I quite like Giovanni as a character (ignoring the HG/SS event moment of weakness there) - he seemed to be an honorable sort, breaking the organization apart after being thoroughly defeated and dedicating the rest of his life to Pokémon. Something about the guy always seemed like there was more to him than just "I'm evil, lol", as opposed to the rest of his team.
Which is more than could be said for the idiot children who attempted to reboot TR in Gen 2/HGSS. But I digress.
Aqua and Magma, meanwhile, are a bunch of ignorant idiots messing around with forces they cannot understand. Yeah, you could call them eco-terrorists. I call them people who have no idea how basic science works, and they honestly needed the solid kick in the head to see straight. Emerald resolving their conflict was nice. OR/AS handled them fairly obnoxiously (aside from turning Archie and Maxie even more memetic than they used to be), but little about OR/AS' handling of the gen 3 story wasn't obnoxious.
Galactic are a cult of personality, plain and simple. There is something utterly lulzy to me about how the basic grunts have absolutely no idea what they're doing (.jpg). I mean, their spouting nonsense and outlandish outfits are indication enough - but the whole "You cannot grasp the true form of Team Galactic's ambitions! ... Hell, I CAN'T GRASP IT." was fucking hilarious.
Then you have the commanders, who are utterly devoted to this charismatic asshole who told them just enough of his plans but not ALL of his plans - because, y'know, he's actually a straight up sociopath who wants everyone dead except himself because when there's no life there's no conflict. Cyrus is actually one of the most fascinating evil team leaders, psychologically speaking. But Gog, his team is a glorious trainwreck.
Plasma are a mixed bag of blind idealists whose idealism led them to pure stupidity and insidious manipulators who are using the front of idealism for their own ends or just follow the head guy with fanatic devotion. Much like with Galactic, the only real source of interest in this team is their leaders (minus the sages, who are divided p. much the same way the rest of the people in the team are) and their poster-boy. Ghetsis was one of the more brilliantly written villains of Pokémon - his calculated actions, the revelation of his real motives and his steady descent into complete fucking madness, which you know that you were responsible for by defeating him. N is a tragic character who manages to inspire empathy even though he's presented as an antagonist stubbornly clinging to convictions drilled into him as a child regardless of the world all over showing him differently... and Colress observes on the side, entirely neutral as long as he gets his research funding, and really, just wanting to see things pan out - I appreciate what he did with Plasma once Ghetsis was out of the picture.
and Flare... well, are a sad excuse for an evil team, much like the Kalos games as a whole had a sad excuse for a plot. Not much to say on these idiots.
(I assume we don't count Cipher and Snagem due to their spinoff status? I mean, Snagem are just a bunch of cartoon villains who are notoriously terrible at it, and Cipher are the Power Rangers Mafia. But yeah.)
So yeah. In terms of sheer plot interest, Galactic and Plasma probably trump the other teams as far as I'm concerned. But I guess there's a special place reserved for TR due to pure nostalgia bullshit, too.