I'd say Team Rocket. I mean, the have the biggest variety of pokemon. Not to mention they have Giovanni, who is not nearly as stupid and short sighted as Archie or Maxie. All they care about is expanding the ocean/land. Giovanni, he wants to to control the whole world.
As for what pokemon they use, if I recall, Team Aqua used mostly zubat and carvanha. What other pokemon they use were mostly water types. As for Team Magma, they used mostly zubat and poochyena, along with numel. Team Rocket, however, used zubat, raticates, physic types, poison types, ground types. A larger variety of pokemon.
Team Aqua and Magma's organization also seemed to be quite a bit shaky. Team Rocket appeared to me to have an iron fist in the organization area.
As for Legendaries, Team Aqua and Magma are trying to wake up their Legendaries. Giovanni created Mewtwo.