Last time I tried to play Endless Sky, I ended up taking a wrong turn and missing a delivery, then got hit with pirates. So I was stuck in the middle of nowhere with no cargo, zero money, and accumulating debt. I quit for about 6 months, because you couldn't delete a character (unless you find the saves and delete them, which is what I did).
Within a few hours, I was flying around in a terrible little cargo ship with no shield, only an anti-missile turret as a weapon, extra cargo and extra bunks. Also, just over a million dollars.
The clipper seems like a much better ship (it had better be for 3x the price), but I'm not sure how to upgrade it.
Edit: I figured out some upgrades: Dwarf reactor, Atomic A250 + A255 engines, a radar jammer, 3 cargo expansions, 2 large bunks, toss the weapons, and put on a slightly larger shield. I guess reverse thrusters would be fun for jumping into hostile areas for deliveries and just stopping at the planet instead of turning around, but that's a bit of an edge case. Pirates already have some difficulty shooting me before I'm gone. I'm picking up every mission I feel like (>500 per ton hauled, or as much as I can get for passengers), and I'll be able to afford a nice escort and maybe a second clipper soon. There's even some extra space for scanners and/or solar panels.