First, I'm enjoying the new factions and balancing that came with the 1.0.15 patch. Very nice. After many hours of playing, I have a couple of suggestions:
1) It quickly becomes annoying to need to keep switching a pirates weapon between his regular weapon and a fishing rod, then back again when danger approaches, then back for fishing, etc. It would be nice to have, for example, the ability to tell a pirate (or group) to fish and let them grab an available fishing rod. Or, a pirate could have an alternate weapon slot and a button to swap the two.
The same is true for using the shovel. The dig button should cause the captain to equip a shovel, if available, dig, then switch back to his regular weapon.
2) There are a number of skills which are useful only to the captain and others which are mostly useful for the crew. Other than trial and error, there doesn't seem to be an easy way to tell them apart. For example, "Treasure Hunter" improves the loot you get from digging. You can teach a pirate this skill, but it seems to do nothing but occupy a skill slot.
Keep up the great work!