Ahoy! I would love to see some form of enemy ship PvE that isn't the skeleton ships. It would be super fun to run into a trading vessel and choose to engage and fight or not. I imagine the trading vessel would have the same types of items as the merchant alliance items and would be easier to destroy (maybe a brigantine or a sloop).
I'd also love to see admiral ships with a bunch of fancy looking folks on it that ride around in galleons or brigantines that drop gold-hoarder type loot, maybe something that is admiral specific like "Admiral's Chest". It would be cool if the admiral ships attacked or didn't attack based on what kind of ship cosmetics/flags you have (ie. if you're clearly a pirate, you're gonna get attacked. If you have the bilge rat stuff, you're less likely to get attacked, etc.)
I just think running into other kinds of ships on the seas would make this game a lot more fun. I really enjoy the merchant quests because it rewards me for spending time sailing and the more activity I can get involved in on the seas, the better!
