My suggestion is to add a bounty system roughly based on systems that other MMO-like games have. As the game is, there is a clear wedge between two of the major player bases of the game the PVP crowd and the PVE crowd. I am of the belief that a bounty system could serve as a way to help both of these types of players out and further flesh out the sea, as well as Athena's Fortune.
The bounty system would be based on unprompted acts of aggression (that the game already tracks for ship commendations) directed at other players. This would include:
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Attacking Players
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Attacking Ships
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Killing Players
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Sinking Ships
It is worth noting that stealing and thievery is notably not on that list, meaning that stealing the goods and treasures off other ships would be more encouraged as it would allow for a player to still take from others and engage in "PvP" but in a much more cleaver and less outright hostile. Which at the end of the day would be what most historical pirates would actually do as most avoided fighting if possible.
It is also worth noting that I said unprompted acts of violence, there are plenty of good reasons to fire at someone else and would not incur a bounty, including but not limited to:
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Being attacked
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Them boarding your ship
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Them touching /stealing your loot
That being said none of these actions would become "illegal" or "banned", they would all remain a completely normal and expected part of the game, but now it would not be nearly as conscienceless.
This is where Athena's Fortune comes in. As it stands, Athena's Fortune is claiming to encourage cooperation and protecting the seas from the aggressive Reapers and their leader the "vile evil Flameheart" but do nothing to actually fight back against the chaos taking over the Sea of Thieves, winning hourglass fights does nothing to actually protect the seas from lawlessness, and the only people fighting the Reapers most of the time are other Reapers.
This bounty system would be Athena's Fortune's way of trying to bring some order to the seas, paying pirates and their own emissaries to go after those who are working alongside Flameheart in his quest to make the Sea's a pirate themed battle royal.
Ships with bounties would NOT be marked like reapers on the map, instead, when met on the sea you will be able to see if a ship has a bounty on it alongside the other ship information when seen through a spyglass, letting others have a general idea of if someone will be hostile or not (though not a guaranty) based on how large a ships bounty is, furthermore it encourages those who wish to partake in PvP know that their is a free target who is likely to fight in their sights.
As an additional mechanic and a further effort from Athena's Fortune to keep the seas safe, At emissary rank 5, an AF emissary would be able to track those with bounties like Reapers can track emissaries, showing their location, but not how large the bounty or the ship is. This would not only enable AF emissaries to earn more rep from their tasks, increase the influence of AF on the open seas, and give PvP players a new way of engaging with combat.
It's not all bad for those with bounties though, in addition to whatever they gained from their aggressive acts, they will now find that there could be a host of new commendations and cosmetics tied to the system, ranging from events like the amount of times you get a bounty, or the actual amount (could even add a leader board / bounty board showing off the largest bounties currently live). If you want to get extremely ambitious, could even repurpose the old arena and turn it into a sort of "criminal port" that can only be taken full advantage of if the ship has a live bounty on it.
As for how the bounty is actually handled and cashed in, it would be attached to a ships logbook, meaning that the only way to cash in a bounty is to sink the ship and return the wanted logbook to an Athena's rep. This would make the process of bounty hunting no more invasive than standard PvP for those being hunted, furthermore it adds the possibility of some ships preying on the ships of bounty hunters to get the valuable log book!
Ultimately this would not majorly effect those partaking in aggressive actions as the goal was to get into fights anyways, but it helps protect PvE players by adding some consequences to random sinking, as well as making crews only in it for the money have to really consider if the loot on a ship is worth the ire of Athena, or is a sneaker approach needed?
As for the actual numbers involved I leave that in the hands of the devs as they would know better than I do in balancing this as a mechanic, though I would encourage that the bounties themselves as well as the rewards for turning them in would have to be significant, as to encourage bounty hunting and making the bounties actually mean something.
As there is already an update soon approaching, and the actual scale of some of the changes, this in and of itself would likely constitute being it's own session, which I personally think would be a perfect follow up to the soon arriving Reaper heavy update, giving Athena fans more to play with and establishing some real resistance to the actions of Flameheart, as well as giving the those who fly the Reapers flag the fight that they are wanting!