Here's an idea I had once but never really have had the time to toy around with. Perhaps someone else can give it a go.
Why not pay your freighter pilots as you would be paid driving a freight truck nowadays; give them a salary? The Nova engine has a "credits per day" function that makes it easy to establish a regular cash flow, and perhaps freighter pilots could continue to receive pay so long as they remain employed by the company, also receiving additional commission from each mission they run - the regular pay you'd receive from each mission, or perhaps slightly less because they already receive daily pay. By implementing a series of company courier missions, each one with a certain crön bit assigned, you could set an "employment termination" deadline, that automatically fires the pilot and removes their daily pay if they haven't finished a mission in the space of a month or something. So long as the bit is flipped that says they are assigned to a certain company, they'll only receive missions from that particular company as well as the regular contracts for passenger delivery. Certain companies could operate in different regions of space; perhaps even shipping vastly different types of goods, which could in turn lead into certain story arcs.
For instance, this is an example of how it could play out:
The player accepts employment working for Consolidated Shipping Lines (CSL) from the mission BBS (listed perhaps as "Employment - CSL", among other employment contracts). This flips the CSL bit set that locks the player out of all other employment missions except for those associated with CSL, which then in turn become available (previously being hidden). The contract details explain how the player should continue to deliver their cargo to their member worlds and offices, receiving a daily pay rate sufficient to cover fuel costs and armaments, if necessary for the region. If no missions are accepted/completed within the space of X days, then the employment contract is automatically terminated, and pay will cease. Missions then default back to the regular set, and employment can be sought with a different company. However, we'll assume the player keeps this job for a while, delivering - let's say - medical supplies to outlying colonies.
A higher-up in the company realizes the player's potential as a hard-working employee, and in a random event, tells the player that he/she now has the option to accept a promotion, requiring dedicated to more-demanding, possibly dangerous routes and missions. If accepted, the previous employment bit clears, and the lower-rung missions are taken away in favor of a new bit, which enables access to higher-tier profit options. The player then also receives additional monthly pay, and maybe stock options (new ships, outfits, etc). Now instead of just regular medicine runs, perhaps the player is put in charge of a team working to relieve a plague world of its dying population, necessitating time-constraining delivery missions or maybe routes through dangerous territory to enable such expediency. As usual, the self-renewing crön tag works as it normally does, and the player will lose his job if he doesn't perform a delivery in half a month, or whatever.
It's a big, wordy way of explaining a relatively simple idea (in theory), but it could make the Nova game a little more involving if you actually feel like you're something more important than being a freelance courier who occasionally ships stuff for United Shipping, or whatever they had in vanilla Nova.
There's nothing saying, either, that this employment strategy couldn't be used to align yourself with certain organizations such as local police, or even branches of the military, allowing better mission specialization among the smaller story arcs. For instance, a person gunning for the local police/peacekeepers could be hired to go and perform routine patrols rife with random encounters and/or even cataclysmic events that lead into one of the major story arcs, eventually maybe going off to work Black Ops and spy on enemy fortresses using a cloaking device, while another player may end up doing the same sorts of missions with brute force and fleet support.
Either way, that's my two bits.
