I always thought it a little odd that you could be max rep with, let's say, merchants and sink their emissaries and sell their flags without repercussion.
Now I'm not saying to change the current system. I understand why it is the way it is. What I'd like is a separate rep system.
This rep would increase when completing voyages for that faction as an emissary. Reach a high enough rep and you could gain access to some form of bonuses. These could be tiered, getting better as your reputation increases.
This bonus would be something you have access to even when you are not flying an emissary flag. Could be slightly better payouts, new voyages, something that would feel rewarding for staying in a faction's good graces.
But each time you sink an emissary, your reputation with the sunk ship's faction will go down some degree. This degree could be based on their current emissary flag rank. As your rep drops you start to loose access to those bonuses.
This could work for Reapers as well. Since they really hate the companies, each time you complete a voyage for a company as an emissary you're rep with the Reapers will start to suffer. Taking flags and treasure as normal would increase it. Now I don't normally sail as a Reaper so I'm not sure what bonus Reapers would prefer for being high rep.
What do you think? Maybe a system like this could be another bonus for captained ships. If so would the rep be tied to the ship or the captain?
I think a system like this could add a bit more to the game as you balance faction reps besides just our current static faction grinds. Could also add a new level of decision making as you debate with your crew if the rep hit is worth sinking that lvl5 Hoarder emissary you just spotted.

