In Sea of Thieves the only ships you will encounter are other player's ships or skeleton ships, both of which are found randomly and inconsistently and in some cases fighting them is not as profitable or as rewarding as just running away. It also does not make much sense that the companies do not have ships of their own and rather only hire people to find treasure for them. Because of that I think that more AI ships should be added to Sea of Thieves.
I suggest that all companies have ships that sail throughout the Sea of Thieves. Although all of the ships of the different factions would be different they would all share some rules in common.
1.These ships carry loot that fits their company.
These ships would have loot in the bottom of their ships that fits their company. They would have different values of loot depending on the level of the ships.
2. These ships would have a crew that would have the gear of that company and would do certain roles.
The members of the crew would have different levels. The first level would have the sailor armor and would do jobs such as repairing the ship or moving treasure below deck if a player brings the treasure above deck. The second level would have the sailor armor except for the jacket which would the the basic jacket of that company. They would use the cannons and would move the sails or raise/lower the anchors. The third level is the captain of the ship who would have the full armor of that company and would steer the ship. All of these levels would attack the player if they are on the ship unless they have another job to do at that time.
3. These ships would not attack players unless attacked by them(with some exceptions).
The ships owned by these companies would be peaceful ships that would carry loot specific to that companies. They would travel on a set path and would not move from that path unless attacked. The ship would consider itself attacked if a player shoots or throws a cannonball of any type at it and it hits or lands within a certain range of it, if the player attacks a member of its crew, if the player picks up any treasure stored on the ship, if the player hits the ship with their ship, or if a player affects the ship in any way, such as anchoring/unanchoring, pulling the sails up or down, moving the cannons or anything else that effects the ship.
4. An emissary of a company will lose emissary points if they attack a ship of that company.
5. Any treasure taken from a company ship will have stolen before its name and you will only get gold without reputation if you sell it to the company who's ship you stole from.
If you steal loot from a company ship and sell the loot to that company you will not get reputation from that. If you sell it to a different company then the reputation will be the same.
The Gold Hoarders ships would travel on routes between small islands and outposts. In the bottom of their ship they would have loot that the gold hoarders accept. They would always have a rowboat on the back of the ship.
The Merchant Alliance ships would travel on routes between outposts and outposts or sea posts and outposts. They would have crates in the bottom of their ship and will sometimes have piles of gold as well.
The Soul Hunters would travel on routes between many different islands. They would have skulls in the bottom of their ship and they will occasionally have skeletons in cages in the bottom of their ship.