My thoughts about this interesting topic:
First thing I would like to see is production buildings. I'd love a system like EVE Online, with a player driven economy where everything is produced by players, and with a realistic "stock market". I think that woud give depth to this beautiful game.
I haven't tried crafting yet, but I personally don't like the labor hours system: i really don't like just clicking the mouse to see goods appearing from nothing. I think that a system based on real time hours and production cycles woud be more satisfying and realistic.
Then I would like to see exploration gameplay and exploration missions, maybe with instanced "secret" sizes on the open sea, and maybe hidden resouces on islands. That would give more variety to PVE and would give more satisfacion on sailing around the world.
I would also like to see instant deliveries replaced by delivery missions.
Eventually I would appreciate officers and refined crew management, as a way to improve ship customization and strategic depth.