The first thing I would like to see would be proper solar/star systems, with planets orbiting stars.
Being able to set star type (color), number of planets around the system (0-12), type of planet, number of moons, asteroids belts and comets, etc. would be cool.
Make it so size, distance, type, etc. would affect habitability.
Also add more species or species customization. Being able to choose species attributes, culture, survivability, etc.
Look up a game called Pax Imperia: Eminent Domain. It did this really well!
It gave you some default species:
Humans who were average.
A warrior species, who excel at combat but are poor at everything but weapons research.
A espionage species, who are good at preventing spread of other cultures and great at stealing other species ships/technology but poor at everything except espionage research.
A research species, great at all research, poor at combat but good at moving in 3D space, so are good at defence.
A builder species, could obviously build everything at a faster pace.
A resilient/breeder species. Excelled at living in almost any condition and could colonise any planet type with no problem. But were very dumb and poor at research/everything else.
But what it really excelled at was species customisation. I can’t remember it all of it off the top of my head but you could set thing like:
Species temperature preference: Freezing, Cold, Mild, Hot, Boiling. This would affect how adaptable a species was to a certain planet, affecting growth rate and economy. Star type, planet type and distance from star would affect a planets temperature.
Research Ability: Setting how well a species completes a certain type of research, Low, Average or High. I think categories included Energy Weapons, Missiles, Shields, Economy and Colonisation.
Species Culture: Choosing a culture would affect how well a species excels at certain things. For example warriors excel at combat, researchers develop technology faster, traders get an economy boost, diplomats excel at relations with other empires, hostile suffers in relations with other species but stop culture spread from other species, spies excel at espionage.
Other traits including being subterranean, which would remove a species need to select a temperature preference.
There were quite a few more options but I can’t remember them.
Really look at Pax Imperia: Eminent Domain, it has a lot of cool ideas in it which I think have been lost in the modern gaming era.
If I get the chance I will re-install it so I can see all the old options.