So today a level 2 Reaper sloop tried to sink our level 5 Order Galleon and it didn't end the best for them, while they managed to escape they did take a lot of damage, I believe they fled to save their own flag rank. It got me think about how not many people (at least in my experience) seem to take a emissary flag; I've entered servers where at most there's one other emissary ship on the tables. Like tonight, there was only the two of us (1 Order, 1 Reaper) but I saw at least three other ships without a flag.
My suggestion is a simple one; have something for the reapers to gain when they engage (or are engaged) by a non-emissary ship and sink it. Yes you do get treasure but every ship is likely to have treasure; but what happens when a ship specifically comes to fight you? It seems out of place that non-emissary ships are exempt from earning a Reaper any sort of rep or reward.
As for the reward, think of it as something like mermaid gems, you have three tiers that signify each of the three ships. It would be something from the ship itself like maybe the nameplate or a piece of the ship's wheel, the map from the map table; something that all three ships have onboard that's usually non-intractable and only spawns if you're not an emissary.
