Vinsmoke Judge

The final (currently known) member of MADS, Judge, was also responsible for discovering lineage factors. Furthermore, he and his Germa 66 kingdom are the only group in the series currently known to be capable of cloning. Judge is brilliant, as well as being shrewd and tactile in battle areas.

Franky

Franky’s intelligence only grows during the time skip, an incredibly talented shipwright who even turns himself into a cyborg. He discovers Vegapunk’s old lab and various research documents and projects from which he studies and learns. These new skills and knowledge are seen on full display in post-time-skip One Piece.

Trafalgar D. Water Law

Commonly referred to as just Law, the captain of the Heart Pirates is also their doctor. The true mark of his intelligence comes from studying to become a doctor from near birth and curing himself of Amber Lead Syndrome.

While he did accomplish this with the help of the Op-Op Fruit, the process still requires an incredible amount of medical knowledge. Even more impressive is the young age at which Law possessed such knowledge and skill.

Nico Robin

Being the last survivor of Ohara, Nico Robin possesses ancient knowledge and skills, which nearly no one else in the series does. Her intelligence primarily manifests in her role as an archaeologist, including reading Poneglyphs.

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Chopper

The first “good guy” on the list, the resident Straw Hat doctor, is incredibly gifted. Chopper’s development of the Rumble Ball proves this, allowing him to expand his Devil Fruit power in ways other Zoans are unable to. His knowledge of medicine is impressive, thanks to his origins as seen in early One Piece and further research mid-time-skip.