Team flare was by far the worst team. They were just a bunch of goofy weirdos until you get through like 75% of the story, then all of a sudden they're a bunch of genocidal weirdos. I'm not saying Aqua/Magma were particularly good, but I definitely prefer them to Flare.
Like has already been mentioned, at least Magma/Aqua managed to awaken their respective legendaries, while Flare had some random kid break in and catch it... That's really pathetic.
Their entire purpose is also very hard to take serious. They wanted to destroy the world so it could come back and be more beautiful... Really?
This. They did almost nothing. They wanted money? You don't have to expose yourselves publicy as criminals to get money. And their biggest plot was to steal a Master Ball. I know they planned to mass produce them if they succeeded, but they didn't. At least Magma, Aqua and Flare had the competence to actually catch the Legendary Pokémon.