Suggestion:
Add some social and psychological aspect to space combat and traveling. For example, low morale from constant combat, losses, casualties, and low readiness or taking unnecessary risks for low rewards, pushing the men in your fleet can increase the chances of mutinies or ships leaving the fleet. (perhaps even a small group of ships leaving the fleet under the command of one of your capable officers to set off on their own if morale is too high as well)
Get to know your crew, officers, and perhaps other people in the game like leaders, spies, contacts and other fleet commanders.
Ships run from combat under low morale and fight to the death with high morale.
Maybe romance? eh... having a family? the main point being fleshing out the human aspect of the characters and nameless masses in-game and it affecting your playthrough and decisions.
EDIT:
The people that have made this game seem to be quite good at designing and implementing game mechanics that add quite a lot of depth while remaining rather simple, keeping the tediousness and chory-ness of those mechanics down to a minimum when you compare them with other titles, while remaining just as impactful, interesting and compelling. It's no wonder it's such an addictive game.
My point is I'm not suggesting adding complexity, I'm suggesting adding "human elements" in the game. I think it would be possible to implement it in a simple way that adds a lot of depth, just like other aspects of starsector, while remaining straighforward. What that would look like, I don't know. I'm no expert in good game design. The examples I gave was just to help get my point across, certainly don't put in anything that I've mentioned in the game, they were more or less verbal diarrhea. If there is a way to add simple mechanics that touch on those human elements, it might further make the game more interesting.