(Out of) Party Members:
Ghosthearts - Don't spawn their ghost companions if they are not in the party (even if you have set them to do this in their tactics options). It is also not in a Rangers default AI (the default AI has been geared for normal rangers it seems).
Actually can someone tell me if there is a limit to how many adventurers you can recruit (I read it is 8)?

Ship boarding:
There are times when a person on your ship stands and does nothing (probably out of perception range of combatants).

Factional Ship Variations:
Have the different factions have slightly different ship stats. Maybe Factions A has faster but more fragile ships, Faction B has slower but sturdier ships etc. Also do ships have a "defence" stat (is that the "ShipAttributeType": "Hittability",)? Might be nice to make the smaller ships more maneoverable (could also be used in the Factional Ship Variation idea)?

Sell Ships:
An option to sell your old ship. Also maybe a way to sell your menagerie (or just delete - mine was bugged, it installed but all pets still in my inventory with no way of getting them into the menagerie).

Trade Routes and Random Ships:
Introduce random ships who (when spawned) will follow a trade route and then despawn at their last port visit. Traders will be trading, Faction ships will be patrolling, Pirates will be raiding along these routes.
Maybe add the chance of the random ships fighting other random ships (and if you attack a trade ship, then a patrol ship in sight will try to engage you)?

Trade Options:
Introduce trade goods to the equation. Each port has an import/export, mioght as well put it to use :).

Crew Options:
You can pay to re-train party member, it'd be nice if you could do this with crew members boat skills.
Also show what class a crew and level a member is.
It would be fun to equip them as well.

World Map Zoom out:
Increased zoom out when in your ship travelling.

AI Character Settings:
A way to duplicate (copy paste) behaviours from one behaviour set to another behaviour set.
IE: Copy from the Fighter (Aggresive) behaviour set "Close the Distance" behavoiur into the Fighter (Defence) behaviour set. This is just an example (I know ther basic behaviour sets are locked), but I hope you, the reader, undertsand what I mean.

ADDED:
Levelling:
It would be nice to be able to level from the character screen (assuming you are in a safe location etc).
While out at sea (or in a tavern - it is needlessly fiddly to have to alter your party just to check to see if someone out of the party can level), the option to level any character you have on your roster - rather than just those in your party.
You could do this through the character screen and clicking on the arrow that changes the party member selected - so that instead of going from party member 1 to 5 it will carry on to out of party members. It would be handy for re-equipping too.

Added Added:
Crew Member Healing :
The option to heal your crew in the city (at a cost off course). Maybe through the supply menu.

I'm pretty sure the part with the ships will never happen, because the ships in Pillars II are created individually. Which means if a ship is destroyed, it's just gone. A complex system like the one you are talking about, would require random generation of ships, to keep the necessary queue filled no matter what. And since that system does not exist in the current game, they would have to develop it from scratch. That sounds really expensive.

@Santiago, shame that, wasted opportunity. I did find a way to have enemy ships respawn, but it is an un-elegant way. However the chap who made the unity console mod came up with a far better way (it is a nice mod btw).

Another thing:
Respawning resources:
With time a place that grew fruit would produce more. So if you "loot" the fruit trees overland, after time they would respawn.
Random wreckages (really low spawn rate), probably near the coast.

See it like this: You, the PC, are not a farmer like Edér. He would not burn the plantation after raiding it. Sadly, the PC is not Edér and doesn't know how these things work. ;)

Well... that would be true for some stuff, but... My mother in law has a small (untended) orchard and, despite me not being a farmer, when I take apples, more apples grow! :)

I think this is more about the "economy" of the game. I can't say I ever had a food shortage. So if I don't have a food shortage now, how overflowing would it be with even more free fruit? As soon as the ship's cook is leveled up, the consumption will be relatively low.

I have not had a food shortage either, i just think it would be nice if certain resources respawned, it would feel more real.

The economy issue... well it is always tricky to get the economy right, especially for an RPG (where you usually start off with too little, then end up with more than you could ever use).
It MIGHT work here because of the finite resources (limited number of encounters/quests which means a limited amount of EXP/gold and items), however my view is this:
Some people like to grind and in this game there is the potential for piracy and trade (which are aspects that certain people like to do).
This game would appeal to far more if the options for those activities were available.
Say in the options there were choices for respawning/random enemies/encounters/resource spawning and trade goods.
They could be turned off by default (this would meet the makers view on how the game should be played and also the views of the... whats the word I'm looking for... let's use traditionalists, while the option is there for those who want to grind or rp life as a trader/pirate/scavanger, which = more happy people).

TLDR?
Options are good.