Devil Fruit users don't lose their powers in the sea just because. It's because someone or something exercises their will or power over all the water in the world to such a degree that any Devil Fruit user largely submerged in it begins to lose their strength.
My guess: Davy Jones, the legend of whom was introduced by Robin all the way back during Long Long Island, described as an ancient pirate who was cursed by the Devil and who lives on the bottom of the sea to this day. As the world of One Piece became bigger and bigger, that little tidbit of information seemed less and less of just a throwaway detail to be forgotten.
Did he eat a Water Water fruit? Does he have a conquering will so powerful that any 'devils' that enter his demesne become suppressed and lose their power? My idea would be something along those lines.
Could he have been a figure from the antiquity of the Void Century, who was consigned to a bitter grave below the waters by the ancestors of the Celestial Dragons? Are there secrets he jealously guards on the bottom of the sea to this day? If he truly spurned the founders of the World Government, that may very well satisfy the legend of him being the 'First Pirate'.