Just some thoughts.
Rockets to be purchased (as in real life). You cannot reload a rocket launcher with minerals. You need actual rockets. Dah!
Water Worlds. Again Submarines. Perhaps your starship can float for a small amount of time before sinking so you have to be quick swimming or travelling further with a Submarine/Nomad.
Let us surf a sun. Strangely you can fly in to a Black Hole but not a Sun.
Something to make Haulers/Fighters/Shuttles more necessary.
48 Slot Haulers are just storage. Exotics have all the power.
Shuttles are useless
Fighters replaced by Exotics and Haulers.
Places where only Shuttles can get (small enough and don’t attract bandits so much).
Can have more on the Freighter/Carrier again because of size.
Inter-Connectivity between them so you can build a "Swarm`
To be able to transport DNA/Creatures from System to System. Takes up Slots Allocation but profitable and not necessarily in Units.
Freighters/Carriers to have 9 usable slots or rather 8 usable slots if you want anything to land. It is daft to have 3 unusable slots.
Systems with 2 Black Holes consuming each other or one or more planets.
Systems with Binary Stars.
Random Rarer Ships so there is no guarantee they will be there when someone else turns up. Stops WWW spoilers.
Some reason to HAVE to go in to caves. Spiders not withstanding getting lost in a cave is a real possibility. I have yet to find ANY reason to take the risk, even if I have 2 methods of getting back.
Accessible Freighter/Carrier Gun Turrets. Possibly limiting slots again.
Exotic Planets to have something interesting to do rather than just be pretty.