The game atm feels...empty. You can fly around ,trade and pirate and build fleets, but there is no purpose other than to just do it. IT lacks a campaign. A story. Something to flesh out the universe.
In order to see how to do that, one needs to look no further than two great games
X3: Terran Conflict and
Escape Velocity Nova.
They both contain self-contained storylines/mission chains the player can bump into.
I'd say that EV: Nova does it better despite being older. It came with a primitive tool one could use to make missions - but it was still lightyears ahead of what Starsector has. Which is nothing. The idea isn't for the devs to craft storylines, rather, to create tools to do so and let players make storylines. Good ones could then be put into the game.
To get back to practical side of things, let me explain how EV: Nova did things - most of it was simple flag checks to display text and do action.
http://imgur.com/BGSB2A mission chain could be started (there was a % chance) by landing on planet, entering the shipyard, the market, the bar ().
One could set conditions - if the mission will only appear in the bar, or any planetary location; if the planet is directly specified by name or condition - like belonging to a faction.
The "missions" could also be set to trigger if you had item X in the cargo hold.
On start, a mission would prompt you with an image/text and options. You could usually decline a mission chain, after which it wouldn't appear again.
Starting a mission chain would set a flag as set, which would activate the next stage. Each stage had it's own conditions, triggers and effects.
A mission stage could be set to place/remove items in your cargo hold, sabotage your ship, spawn enemies (various conditions - it could spawn a few corvettes taking off from the planet you just left for a quick getaway, or could spawn a fighter fleet at the nearest pirate base that would actively look for you, or an ambush at half point of your journey, etc..)
A lot of powerful things can be done with simple methods, but for someone to do this for Starsector, it would require a LOT of wrangling with java. Ironically, a 30 year-old game has SS beat in user friendliness and mission coding.
This is something you really should work on IMHO, as the profits are more than worth it.