Anton's abilities were indeed strong; he was the type of all-round special agent who you could just throw any task at and then not have to worry about it anymore.
Anton's abilities were too strong, and his style of doing things was reckless and unbridled, which put a lot of pressure on Yang Yi, the boss—it's not easy having an underling as overpowering as Anton.
But the boss of the Organization of Water was Yang Yi, not Anton, not Brian, but Yang Yi.
True, Yang Yi's capabilities didn't match Anton's, but if Anton wanted to be in the Organization of Water, he had to listen to Yang Yi. It was a matter of status, not capability.
If Anton thought he was better than Yang Yi and could ignore Yang Yi's orders, then his options were to either kill Yang Yi and become the boss himself, leave, or die.