Team Rocket all the way ! For many reasons... First, their boss. I prefer Giovanny way better than Cyrus, that was an annoying boss to my mind. Then, the member's outfits. TR's outfit's badass, while TG's one is just ... Uh... Ugly. The blue hair bowl cut. No, no, no.
Then, their goals are both interesting. TG's goal is more original and more inventive. TR's one is simple. But more devilish, in the sense that members are bad people, their aim is bad, they know it. TG's members want good things, but act in a bad and crazy way to obtain them (which show how weird they are xD). And once again I prefer TR on this point. I'm for the devilish side.