One of the issues that has come with being able to dive to voyages, is there seems to be less people sticking around on a server. They do their voyage, they turn in, then peace out to a new server.
There really should be some incentive to keep your boat going for as long as possible.
I think there could be a few ways to incentivized this.
1: Have a "Server Longevity" multiplier. If you are on a server for just 30 min or less, you only get 75% of the value of your loot. After 30 min you get 100%. Once you hit 90 min you get a 1.25 multiplier on all loot/Rep, and after 3 hours hours you get 1.75.
2: Have a "Ship Life" multiplier... So the longer you keep your own boat afloat your loot has more value... probably follows the same timeline as the upgraded Journals. Starting at 1x, and going up to 2x.
3: I have to give credit to @PaulKenobi85 for this one, but have Distinction Levels for your emissary flag. Basically give reason for players to keep the flag up longer, and not cycle it. Each Distinction Grade will award you with a increasingly more lucrative Emissary Quest. In Turn, the Emissary Flag will increase in value for each level of distinction. For the crew of the ship, when you lower your flag, it would just go up by 5k for every distinction level. However, it would become much more lucrative for any Reapers that are able to snag it. Maybe make the flag become more and more ornate with each distinction grade.
Basically: It would be beneficial for the game to push people to stick to the server they logged in on, and give a solid reason to have them keep flying their emissary flag.
While there will still be people who hop looking for events to steal, this would give a monetary gain to stick around for a bit and just play the game as it was intended.