For my thoughts on what I'd like to see added:
1. Crew Management. So you lose crew in a battle. You should therefore have a depleted crew coming out of the battle and in open world. You will therefore need to go to a friendly port (or neutral) to replenish crew.
2. Supplies. I'd like to see the need of supplies. Food, fresh water, rum etc to keep your crew alive, fit and sane on the open seas.
3. Ships log. A log that you can record ship spread and bearings, locations at times, spotted sails, trading Information from ports from your last visit (inc. Prices)
4. Group icon to be replaced by a pennant on your ship. The game is stunning. So having a whacking great icon above friends ships is a bit of an isore. Using a pennant instead would do the same job but it will add the need of communication and staying in sight of one another more than before. Plus it'd look freaking awesome.
5. Signal flags. Useful to communicate in group, port, small and large battles. Means captains will need to actually pay attention to squadron members to succeed. Of course with friends Teamspeak will always trump this but for the ones without, its a useful and.immersive addition.
6. The ability to close gunports. Trader vessels with open supports? Why?
7. Ability to name your ship at purchase. Or, as was done, to rename captured vessels.
8. The need to crew captured vessels back to port using a skeleton crew as was done. Having them magically appear in your capital is hardly immersive. Especially when it contains cargo you can sell but can't carry on your current fleet. Adding captured vessels to your fleet and using its hold.
9. Probably a bit far fetched this one but the ability to see and/or use a dock at ports. Giving ports variation would add much more to them and being able to dock would be far more appealing than just sailing up to a port and clicking enter. Unknown if this is possible.
10. I don't know if this will ever be a thing long term but land battles to capture forts in the long run? Having the need to damage defences from the sea and then land to take the main town.
11. The possibility to see boarding action instead of just a menu (aware it's beta) but would look awesome.
12. Clan made flags
... I'm aware it's beta currently and I will admit I don't know how much the devs are putting into this game but these are just some of the thi.vs that would add much gameplay and immersion to the completed product. Any thoughts?