I don't think anyone has done a proper living breathing galaxy in single player yet - the programming and the mechanics the AI have to keep track of would be terrifyingly daunting...
X-series hid it well behind a laundry list of distractions while EVE let human players create the dramas. Elite is basically a 3D, MP version of Starsector atm and both games are suffering from the 'why should I bother' symptom.
It would be interesting how either games approach this issue - especially since SS doesn't have the MP crutch to lean on. It also makes the combat portion of the game seem like such a small cog doesn't it?
It is definitely a hard thing for a game to do.
One that comes to mind though is the the Prophesy of Pendor mod for Mount and Blade: Warband.
It starts off like Starsector in that you have just a small group of low level soldiers and your character is rather unskilled. But after working hard you can get a decent army going and you have a lot of options on what you can do.
Do you want to trade, be a mercenary, hunt bandits, join a faction? You can buy buildings and land to make passive income, hunt roving bandits and random horde like enemies, such as the snake cultists or something like that.
But the game is just starting with all that! Because you can eventually take over a city and found your own faction. That is when the options really open up. Do you ally with other factions or go it alone? You can wipe other people off the map entirely or simply engage in politics to ensure no one gets too powerful. Or maybe you'd rather just go questing for the best items and the favor of the elusive elves. You can do that too.
The game also allows you to upgrade your cities, train your soldiers, found knighthood orders and many other things.
So I guess those sort of ideas is where I see/hope Starsector is going. I think it is on its way there and just needs time to mature.