I know this kind of goes against the social aspect of the game, but a little more self sufficiency.
I think crewing the ship with friends is awesome and all, but I feel there should be a way to use different cannon ammo types when uncrewed as well. Or even just to hire a crew when sailing solo. Something to kind of level the fact that a lot of the npc enemies can shoot off different shot types while I am stuck with roundshot.
Also on the ship system, definately a custom flag option. To keep it kid friendly just have a stock of different "parts" of the flag (similar to how the naming system is done) and voila... individuality on the high seas... who knew!
More weapons. I feel the game is pretty balanced as it is now but for example, it would be cool if you could purchase a cutlass that did poison damage... or fire damage 10% of the time. Nothing too drastic but some variability would keep the game flow interesting.
I think it would also be cool if you could fire cannons from the forts in say kingshead at boats in the harbor. Along with this, I'd like to see ships on the horizon, or in the harbor when on looking out on the sea. I know this probably will create crazy lag but it'd be cool ;P But definately with the forts, I think it would be fun to attack from the sea (as you do in Sid M Pirates)