Skills will refer to the actual skills, not special abilities, that are obtained in the Growth Chart. You can tell what these are by finding them as the bronzed sun icons. There are quite a few on the Beginnings map, as well as at least one in most of the characters' specific maps too. Simply level a skill up to their maximum capacity to obtain this trophy.
Early on, I'd suggest just focusing on clearing all of the Beginnings map, since you need this for another trophy anyway. Otherwise, if you get far enough, Brothers' Sake Cup from Sabo's Map would be beneficial, as would Cat Burglar from Nami's Map. BSC increases the amount of Crew Experience you obtain at the end of an episode, while CB increases the amount of Berries by an insignificant amount.