[Ulzgoroth]

One thing is that refitting ships isn't that attractive a thing under the usual Spaceships system. There's not much of the steady spectrum of interchangeable parts like you typically see in the games you're modeling this on. If you leave that as it is, the fighter pilot's riches will...buy him the best fighter on the market, probably new rather than by upgrading his starter bit-by-bit, and plenty of fuel and AM warheads if he wants them, but it just won't take him all that far without moving up to a larger hull.

If they're working independently, their pay is going to be substantially affected by the size of their ship, in line with the costs. You should be earning your appropriate return on capital, so if the freighter costs an order of magnitude more, it'll earn about an order of magnitude more for similar time and risk. Of course, if the freighter and science vessel do low-risk work and the fighter pilot runs risks and succeeds, the latter may reap greater riches, especially after expenses. A freighter running safe, well-trafficked routes can expect to make basically no profit beyond interest.

Similarly, if they're working together, they probably shouldn't be dividing the take evenly. The fighter pilot isn't bringing an equivalent resource contribution, he shouldn't get an equal cut of the revenues. You could make this the PC's (or players') problem.