There's a reason I prefer Team Rocket over the other teams. The Rockets are your seemingly-generic mob, but they like to work behind the scenes. They have spies everywhere who are seemingly normal people, but when no one is looking, they start stealing secrets. They may go after Legendaries, but it's really rare. The only Legendary they went after is Mew, and that was to clone it. (Can't say for sure if this applies to the games as well, though.) Most of the time, they run black markets and get their revenue that way. It also helps that their boss is a public figure and rich to boot. He has the money to hide everything from the authorities, if not bribing them in secret.
I think Team Rocket was based (rather loosely if not completely) off the yakuza, which is like the American mafia. The other teams seem to be more based off of terrorists and corrupt animal rights groups. They're annoying as all hell, but the yakuza/mafia are rather powerful, clever people who work in the shadows and have lots of connections. It takes a lot to disband them. It's rather unrealistic for a ten-year-old to disband them on their own, but hey, it's the Pokémon world. Anything goes, apparently. Team Rocket would've realistically kidnapped and held him for hostage, if not downright murder the kid.