>>28411813X/Y felt like it could have had the darkest plot yet. Team Flare were basically Nazi's.
But Game Freak realized the themes of the game (Life/Death, exterminating the unpure, ect) were too dark, so they pasted an overly friendly paintjob over it all, which spoiled it. Team Flare, despite having the darkest motivations, are the goofiest and least threatening team yet.
Such a shame, coming off of Rocket/Plasma in HG/SS and Gen 5. Those games actually had points where the villain teams felt threatening. Cyrus in Galactic was also really good.
As for the Hoenn games, I never really liked Magma/Aqua. Magma never felt like legitimate villains at all. Hell, in AlphaSapphire, there's not even the slightest hint of them doing anything wrong. Aqua were dastardly pirates, which was something, but Magma always seemed to just be chill scientists that always had the worlds environment in mind. Granted OmegaRuby does more to villainize them, but still.
But now we have Skull, and Aether. Definitely far more interesting than Aqua/Magma/Flare. If they are executed well, they could be the most interesting "Teams" yet.