So, I think it would be interesting to see some high-combat factions each have one base become a place to get extremely difficult missions. For these missions, players would have to fly through 1-2 jumps, increasing their risk of encountering hostile players along the way and decreasing the ease of returning to the waypoint and base. This travel time would be factored into the mission reward, for increased bounty.
These missions' npc's would drop 2 pilots, and nomads from these missions would drop 2x as many remains. Credit card and other commodity rewards would also be increased. Alternatively, for easier implementation, rather than having different bases for each faction, perhaps a single base, accessible to everyone, could be placed somewhere, providing missions against an extremely powerful faction such as cultists, nomads, or phantoms.
$6-10m missions would put players against highly effective NPC snubs and battle freighters. They would have a 6x armor multiplier and top-of-the-line equipment, with missions closer to the higher end having a higher chance of encountering SHFs and Bombers. There would also be a chance of one of the waves being a single SHF with a 15x armor multiplier and gunboat weapons (If that's okay?), while still utilizing torpedoes. Enemies from these missions would drop a total value of $1m in credit cards for the easier $6m missions, while the harder missions with SHFs and Bombers would drop up to $5m in credit cards.
$10.5-13m missions would put players against improved NPC gunboats. These would have a 5x armor multiplier, and the AIs would utilize thrust and turn much more, like fighters. Missions closer to $10.5m would feature mixtures of gunboats and fighters in each wave, while missions for $13m would feature 4-5 gunboats per wave. These missions would drop up to $10m in credit cards.
$13.5-16m missions would feature improved NPC cruisers. These would have a 5x armor multiplier, and the AIs would use thrust. Each wave would consist of 4 cruisers, a gunboat, and 1-2 snubs. These missions would drop up to $12m in credit cards.
$16.5-25m missions would feature improved NPC battleships. These would have a 4x armor multiplier, and all battleships would receive the largest battleship shield (as NPC battleships do not dodge shots, and smaller size provides them little advantage). Missions for $16.5m would feature 2 battleships supported by a cruiser or gunboat, with the rest of the waves being assortments of other ships, while missions closer to $25m would spawn 2-3 battleships, 3-4 times in a row. These missions would drop up to $20m in credit cards, apart from nomad missions which already drop valuable remains.
At first glance, these rewards might seem high, but let's keep in mind that these missions are going to be difficult, and will often require the help of additional players, splitting the rewards. Additionally, in the time it will take to fly through 1-2 systems, do the mission, and fly back, players would be able to earn more by hauling ore. These will, however, at least turn missions into an alternative way of earning credits, and would likely result in players working together to take on these missions.
I know this would be some work to implement, but people would likely enjoy this.