Currently every star system feels the same, and there is no difference between locations around stars.
Could we have varying enviromental conditions, such as higher temperatures in light when closer to a star, more radiation hazards and such?
Also, different star systems should vary in parameters, like there could be more active and unstable stars that could cause their own problems, like the probability of solar flares that would heat up the ship and radiation bursts that could knock sensitive electronics out (and fry the crew outside the ship walls)?
There could also be other enviromental random events, like meteor storms, that could puncture the hull if you don´t have shields up, and risk the crew outside of the ship.
You could have some kind of warning before the events, to try to get the crew inside to safety.
With higher risk could come greater rewards, like in Star Control 2, where the best mineral deposits were usually around hotter stars.
Also, maybe you could attemp to "farm" aliens and alien eggs for food or resources? The risk would be ofcourse an alien outbreak on the ship.
And could we have a possible alien infection for the crew members that were captured by aliens, the longer they were captive the higher the risk of having an alien growing inside them, and that could be detected and attempted to be removed by surgery, that would also risk them dying depending on the doctor´s skills.
Like it said in another space game, "space isn´t a friendly place, in fact it is unfriendly to the extreme".
