All I can say is that I definitely have Team Rocket ranked as last . They're just a bland mafia whose goals don't even match their doings ( like someone up there already pointed out, anyone can catch a slowpoke and cut off its tail. We don't even see them try to catch a legendary or something, we just keep seeing them trying to control pokemon via radio signals without doing much with it)
Flare.... well its a cheap knock-off of team rocket, really. If you want only the beautiful to remain in the world, why have ppl pay 5million pokedollars to join your team? Will that make them beautiful? Will it clear away their ugliness? No it won't. In the end their goals make little sense as well. Sadly, the only thing flare has going for them in my eyes is Lysandre's theme. I think it's one of my favorites.
Character-wise and plot-wise, Team Plasma and Galactic are my favorite. They felt like they were a threatening presence for once, with Plasma making for one of the best games out there (esp bw2) . Galactics had me with their explosions and admins + cyrus. Also, I like how Cyrus was duping even his own organization in the end
Goal-wise, my favorite is Magma. Sorry, not Aqua because to me, Aqua's goals lack sense. Expanding the sea would only provide living conditions for more water types, disregarding both humans and the rest of the pokemon. In my eyes, Magma is the "canon" team, since it's completely understandable that s1 would like to expand the landmass, making room for humanity to develop and whatnot. Maxie didn't see the bigger picture either, but yeah, goal-wise, I like the hoenn team most.