Customization of ships: Please listen to this one especially capital ships. The upgrade on capital ships with experience does this a little bit, but my preferences would be as follows. Allow customization of ships especially capital ships. The upgrade on capital ships with experience does this a little bit, but my preferences would be as follows.
Experience increases overall performance, an experienced crew fires faster, is more accurate, can calculate a jump faster, repairs hull damage faster, etc. Basically an experienced crew can do more with the same ship.
With resources you can buy upgrades to your capital ship (maybe even your non-capital ships), those upgrades have to be purchased at a capital ship yard, and your ship can’t fight while upgrading (or maybe just can't leave that system while upgrading).
The upgrades/customizations would be how you get better weapons, better shields, etc. Upgrades would also include special abilities, some unique to the particular empire. These could come from race specific traits or buildings that are built on planets of certain types. I.e. if you are Vasari then you can have an ion cannon that requires an heavy metal factory on a volcanic planet moon. Etc.
Actually allow players to build or design there own cap ships, even bigger than the in-games ships. Obviously this would be in hi tech levels. But could be achieved though larger tech trees. Very good for longer games. I would like to see more types of ships, other than the mirrored ships of each faction.

Invading forces: for planet attack’s. Jump pods!! Then you could conquer the planet while doing a minimal damage to the infrastructure and other important buildings etc. Then the planet would be back in operation for a lower damage to the planet, and conversion of exciting slots to your side.

Earning squadrons: I know - this is a game - but to be "realistic", if a cap ship is going to have squadrons attached to it, the cap ship should start out with them. Adding a bay for squadrons would involve massive restructuring of a ship and training of its crew. I find it a little silly for a cap ship to be out in the middle of nowhere and all of a sudden, in the middle of pitched battle, the ship has automatically carved out its insides to support an additional fighter/bomber bay. The cap ships should either start out with the max slots for fighters/bombers, or should involve returning to a repair facility to have them installed. Maybe this facility could also be where you would change weapons slots or armour type of older cap ships?

Larger Planet involvement: More orbiting bodies, that have in-game effects. I.e. Moons increasing overall pop of a Planet. Or rings adding more logistic slots. A more planet surface scale related aspect of the game. I.e. building factories, civilization communities, missile bases and troop barracks as defence. And planet type bonuses. I.e. heavy metal factory on volcanic planet. Mineral or spice factory on desert. Antimatter factory on ice planet. Maybe incorporating the moons to help here. I.e. Ice Moon or Desert Moon. I'd like to see some more DEPTH like from Galactic Civilizations in such things like adding the availability of building SEVERAL different types of structures instead of just a few that add different kinds of bonuses to Planets or an EMPIRE.

Militias, vigilantes and bounty hunters. I want to see my citizens take some initiative of their own. How cool wouldn't it be to be defending your home world, when suddenly you find a civilian ship fighting alongside you because your local Allegiance is 110%? Or have opportunistic NPCs with access to ships and military hardware attempt to take the 'pirate problem' into their own hands. Or even rebels. We have these, but I'm thinking more along the line of having terrorist attacks by your own citizens against you, depending on your local Allegiance.

Planet-based defences: (As above) Reminiscent of the Rebel Ion Cannon in Empire Strikes Back, planet-based weapons that could strike at capital ships.

Ground forces: They may not even have to be such a big thing, but if you could have boarding crew’s, there could attach themselves on the site of an enemy ship, and cut right throw the hull, and then fight their way in and take the control over it, that would be cool. I would love for the officers to have rank’s and the ability to raise in these ranks, and then be able to do more complicated and tactically demanding missions.

Battle enhancement: say you have a level 7 Vasari Kortul Devastator- you could tell it to use the following special abilities in order whenever in battle: Volitile Nanites, Power Surge, Jam Weapons, Power Surge, Disruptive Strikes, Volitile Nanites, Jam Weapons, Power Surge, (repeat). It would add another strategy layer to the game- maybe it is too much. Taking a page from SE5's book, I'd like high-end options like blowing up planets and stars, constructing artificial worlds, creating new phase lanes or quite simply building ships that don't need phase lanes. I'd also like to see STL travel between planets. A possible implementation would be some kind of super-ship that can only travel STL.

Moving ships would be great, SINS has too much of a WWI RTS trench warfare system (run up, dive into a static position, and open fire until retreat or advance -wash, rinse, repeat).
Better planetary development -manageable cities/planet (SIMS WORLD???) and improved tactical systems (battle stations, hangars [more fighters/bombers], weapons on all orbital with tactical systems being feared] such as orbital batteries that install-pop frigs/cruisers.

Tech trees: Add more variety to the tech tree, and larger more race specific. Most of the techs seem to fall into +% to something. It starts to feel pretty stale after a while. Needs more abilities/ unique traits, instead of just stat increases. More logistics and tactical options available in the late game. We have super weapons. How about super-installations?

Simplify logistics/tactical slots: To my way of thinking, logistics and tactical upgrades for a planet could be done differently. I think that planet populations of a certain size should be able to support N number of logistics/tactical platforms. So instead of upgrading log./tact. slots for a planet, you would do your best to upgrade the population. Log./tact. slots would be determined by the size of the planet and the size of the population. I'd also like to see the implementation of planetary defence fleets, unable to phase travel and weak compared to other ships, but available. Make them take up 1 tactical slot each. I'd also like to see the ability to interchange between the amount of logistic slots and tactical slots per planet just in case you'd like to make certain choke point planets absolutely fortified but at the cost of sacrificing its logistic slots down to a minimum of just the resource asteroids surrounding the planet. I would like to see star bases/space colonies. I would like to see the ability to claim neutral systems by sending in a deep space construction frigate and building a space station. This would make it possible to properly guard wormholes, stars, gas giants and other non-colonisable. They would, of course, only be a shadow of a 'proper' colony - maybe 5 population, max. 10 tactical and 4 logistics slots, 1 level of exploration.