One thing I've appreciated in MMO's is the reputation leading to (un)favorable interactions from the respective NPC's ranging from "shoot on sight" to unique perks and rewards. Since the skellies and ghosts are minions of Flameheart, what if gaining a certain rep milestone, like the skelly curse, results in said minions from attacking? Since that eliminates combat with most, if not all, the mobs on the map, the offset would be decreased favor from the other emissaries in which they would refuse to do business and set numerous bounties on you for players to retrieve or for NPC ships to spawn and attempt to kill you, similar to the skelly ships that randomly spawn on you. Basically, once you're friendly in the eyes of the mobs, the rest of the NPC world has it out for you and pretty much every emissary will send a ship to hunt you. The more rep you have with Reapers, the more ships the factions send. It would start with sloops and once you cross another rep milestone, you start seeing brigs, then gallies. It stops when you log off or start over in rep.
The Athena faction is one who're meant to be the "good guys," so that could mean the Sovereigns could offer bounties on players. Adding a discount as a reward would be helpful as Athena cosmetics seem to be the only ones costing millions while offering nothing truly unique other than you and your ship can be a glowstick. The DA sails offer the biggest tactical advantage, making it the only thing worth grinding for compared to the rest of the stuff they offer.
We're given a whiff of rep consequences - and I use that lightly - in the form of the Sovereigns denying Reapers their bonus. The Sovereigns are supposed to be the equivalent of the East India Trading Company from Pirates of the Caribbean, unless I'm mistaken on that, which means they could have it out for the Reapers who calls themselves true pirates while burning and looting anyone in their path. This puts all the other factions at odds with Reapers, making them either the easiest to grind because all loot is acceptable, or the hardest because you could theoretically have the entire NPC world attacking you at any given moment.
If people were to ask if this would affect the pirate legend grind, it could be an alternative faction rep. Athena and Reapers have two separate faction grinds so it wouldn't be impossible to make the other emissaries have one. This could mean adding Sovereigns as a faction to gain favor for as well with their own set of rewards.
I think the seas are empty as they currently are with only 6 ships on a server at a time with the occasional skelly ship that may or may not attack you, depending on if they spawned on you or were a random spawn halfway across the map. Grinding rep is fine and all, but I think it should mean more than just another stack of titles and cosmetics that hardly anyone utilizes. The biggest downside is how one grinds rep for the other factions once they decide they want a taste of being on the other team. It's hard to look favorable to a faction who wants to kill you first chance they get, but the captains voyages could be that way out. You buy the voyages of the faction you want to impress and gain rep upon completion. Another method is perhaps a reset option in the emporium where you pay to have your rep reset to zero and start over. The entire premise is that grinding faction rep should come at a price. Right now, the only consequence is being hunted by players for your emissary flag, but that's not influential to a faction's perception. Now, if that were to be influential, it would add a dynamic where a faction looks favorably or unfavorably upon you depending on how many voyages or respective flags have been lowered without being sunk.
There are many more details I could add as well as details that I don't have thought out, but I think there could be a rudimentary version to implement and expand on should it be feasible.
