Honestly, it would be a huge task to undertake. A developer would have a number of important things to work around, like water physics (and the actual look of the water), boat/ship physics, probably a living and changing economy, making ships fun to operate given their slow speed and long travel times (you can't just skip every time you set sail, or have a sea battle every time). Then there would be whether they would add layers of micro-management to it (ie crew and supplies/cargo). Multiple types of battles (ship vs ship, crew vs crew, both at the same time?, atttacking ports from sea, attacking places on foot etc).

There are other things too that I can't think of right now, but again, it would be a huge task.

However, if a dev could get everything right, whilst not skimping on content, and giving it a good polish, it would be one hell of a game.

edit: thought of a few more: finding a balance between swordplay and gunplay. And how it would work when the player with a sword comes up against enemies with guns. Also, an actual swashbuckling system instead of just slashing until someone goes dowm.