1. More In-Depth Economy
Only tax is stable and other major economics like spaceport or trading is too unstable.
It is due to the fact that there are only final product-ships which makes private sector running
But, people buy not only ships but also consumes electronics, foods, etc.
So even if mining ships or freighters don't get destroyed, people constantly consume resources and products from the facilities, so making trade network stable even in later games which empires have stable resource supplies.
And also, just making weapons directly from resources is not realistic.
Because you first have to make some basic components like crystal lens, supercapacitor, software, etc to make a single laser cannon.
So, making basic factories produce some basic components from resources, and some advanced factories produce advanced components from basic components, and final products are produced is more realistic.
It can also make trade network more stable I suppose.
Also, enable planets to have modules like factories, construction yards, weapons, farms so colonies aren't just tax and resource suppliers.
2. Make stations, ships to have actual population in it
In almost all science fictions, there are cities in giant spaceships or stations.
So, enable building specific living quarter modules in ships and stations to actually have population in it and you can get taxes from them.
It makes colonization not obligatory, and small empires can actually compete with large empires with well-developed space cities.
It also makes economy more stable because you can cut down maintenance costs for just allowing private people to live in.
Also, it can make pirate play more enjoyable because building pirate stations will not be painful to economy.
3. Improved leveling/naming system for ships and troops
I don't like current ship captain system because it allows multiple captains in a single ship.
So, allow all ships to have a captain, and all ships to level up as troops do.
Don't allow multiple captains on one single ship.
And also, each troops must have an officer which levels up.
Make all ships and troops to have unique names not like "ABC MK1 123"
I suppose we need a different characters menu because there might be so much captains or troop officers in later games
But, implementing these features can make players to enjoy RPG style gameplay.
4. Allow empires to build an ultimate capital ship
Just allow limited number of capital ship that has no size limit, and that can be built only in planet which has specific facility.
So, it can toe-to-toe with gigantic spaceport and makes a chance to win a losing war.
I suppose it will make later games more interesting, instead of overwhelming or being overwhelmed games.
5. Make more ship roles, and make all ships useful.
In later games, just a fleet with large group of battleships is capable of destroying everything and doesn't die.
Small ship sizes like escorts can barely scratch shield and get so much losses.
So, make more category of ships(Like Frigates divided into short range frigates, long range frigates, main battle frigates, electronic warfare frigates, repair frigates, special ops frigates.. etc)
It will make AI to design ships more effectively.
And also, weapons should be much more diverse. Researching a single laser cannon should enable players to build multiple types of laser weapon(like small, medium, large, super) Making large sized laser can barely hit a single escort, but small sized laser's hit will barely scratch cruiser's shield, will make combat more dynamic, not like a huge fleet of capital ships always wins.
Other modules like hyperdrives shields, or armors should also be diverse, so hyperdrive for capital ship cannot be same warp speed as escort.
6. Enable another fitting option - just assign a ship or station to fit
Current designing enables us to make just "standard" ship for empire, but If I want to make a ship or station to perform unique role, it is too difficult.
So, make another option to design a unique ship or station, so it should retrofit to latest unique design, not latest standard design.
7. Enable ships to battle in a deep space area.
When two fleets collide in one area, you must have a chance to fight, just go through, retreat.
So, you will have chance to cut enemy fleet before reaching your system.
And, in deep space, add some environmental factors like gas cloud, asteroid field, magnetic field to affect ship performance, so you can actually use those environment for advantage.
8. Warp gates?
In the distant world galaxy, even faster-than-light travel looks so slow.
Enclave colonies are vulnerable because your colony will be lost before main fleet reaches.
So, building an warpgate which enables traveling to distant system instantly is a significant strategic advantage.
With technology of faster-than-light, why not?