This is my first post on these forums and I would like to share some of my ideas with you.
I apologise if someone has already come up with these ideas.
1, Ships dock at Starbases - all ships docked on a starbase would act just like ships orbiting a planet. Some starbases could even make ships.
2, Soldiers - each ship you launch could have people onboard, the bigger the ship the more people, and the more people the stronger the ship, for example, you launch a medium classed ship with 60 people on board compared to a medium classed ship with 80 people, the second would be better. But you cant just put anyone on a ship, maybe each planet could have a special building were people train to work on ships? Maybe also an option to name the captain of each ship?
3, Shuttles? - another idea is that all large ships could maybe have a few shuttles with basic weapons? Or shuttles could be used to transport people between ships? Maybe if you dock a shuttle onboard an alien ship, it improves relations between the 2 races?
4, Invasions - more invasion technologies are needed! some that blow up planets, some that leave them uninhabitable, some that wipe out complete populations and leave a ghost like planet?
5, Tourist vessels - this idea hasn't really been thought through, but maybe tourist vessels just like freighters that send people between planets? It improves the economy of the other planet and improves morale of your planet. You can also set a price on tourist ships? for example it costs 1bc to go to Drengi? maybe 0.1bc to travel to a planet not as good? and the higher the price the less people would travel there, but all proceeds go to your race? (This wasn't explained well so I hope you understand

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6, (I know i've read this somewhere) Imrpoved ship builder? - You can add a bridge or a medical section to ships, you could even add crew quarters and customize the ships inside the hull, each bit could add something to the ship.
7, Embassies - If 2 races are allies, then a embassy could be built. If you build an embassy for your allies, then it could work to keep relations at a high and improve both morale and economy of both worlds, especially if tourist vessels go to the world with a embassy on it (See tourist vessels).
8, Events - More major events, maybe even one with a all powerful being appears and starts destroying everything which goes within a few sectors of it? For example, a huge worm like creature that originated in a star, the star grew bigger and so did the worm, the worm destroys all planets around that star, and any ship that goes near it it can destroy, so it would take either a very very strong race to destroy it, or everyone in the galaxy could team up and fight it.
9, Break enemy alliances - Very often I find myself at war with an enemy simply because of who their allied to, and quite often I dont want to fight them so I straight away ask for peace, wouldnt it be better if there was a way you could say to an enemy, we would make peace if you break your alliance? (another idea not explained well, so I hope you understand).
These are just a few of my ideas to add depth to the game and allow you to make each game different.