Warning Superpost Ahead
The tech tree sections should be broken down into two sections. The first is the same for all races and the second is race specific. Just renaming the tech is transparent when the stats are exactly the same, so be blatant about it. This would let you focus on your development and balancing of the racial technologies since the general is automatically balanced.
Another modification to research should be an icon change if you are going to keep the stacked research. A little green arrow in the upper right corner to indicate that you have exhausted that upgrade would be really nice.
Each level of technology should take much longer than its predecessors to research but this should be reduced by the number of research labs you have. A level four technology with the bare minimum four labs should take twice as long as a level three with three labs. This would space out research a bit and add a research development path. You could also include race specific (or non) technologies that reduce research time.
One time artifacts that give you a random technology that is currently available for you to research.
No free Capital Ships at the start of the game as a Game Option.
Increase the shields and hulls of cruisers by 10% and Capital Ships by 20%.
Filter the audible warnings that a fleet is being attacked when it is a trade ship as a Game Option.
Constructions that combine military and logistical capabilities using slots from both (see #7 below). They should have the same slot costs with a slight (10%) saving on resource costs, with higher hull/shield ratings (if any).
Mobile defensive structures.
More artifacts that are randomly chosen at game generation and then randomly distributed. They could be linked to a story line, so that uncovering them brings up some historical story and point to the possible location (no names, just hints) of two other artifacts.
You should be able to give allies a planet/ships.
When be asked to do something for a race there should be two options provided for success. One should be a strike mission and the second should be a payment that is relative to size of the empire asking (larger require more).
Diplomatic Surrender so that the race continues to exists but they have to turn over all their artifacts to you (that you do not already have) and agree to never attack you again. This would be good if you defeat the vast majority of their fleet.
The following are my agreement with all those above
1)Research Exclusive Pathing
2)More Research Topics with more variation
3)Cultural Effects Reworked
4)More Ships of all three classifications OR a new Class (Dreadnaught)
5)Some Customization (cannot be full with this game design or it would be a nightmare to design but three or four slots across the levels)
6)More levels of defenses mainly passive to increase planetary survival
7)Outpost/Starbase that combines defensive platform, trade outpost, and refinery.
Adding Moons, and a lot of other objects to the game, even with a low poly count would make this game much less likely to run well on the highest settings in large games. If this is being considered please make it an Option that we can toggle. Not being conceited, but my system could handle it, but many others could not. These moons should not be colonizable (A Pop. of 1 = 1 Million) since they would be wiped out ten seconds into a raid. They could be used to mount special planetary defenses, like an upgraded weapon (extreme range and triple damage) OR shield system (covers both the planet and the moon from all damage for a limited time - 60s).
Artifacts should not be on the market. If you sell one then an enemy could buy it and use it against you. You would keep them even if you have multiples of the same (which I have never seen). What would be good is the ability to give one to an ally thereby forming a permanent alliance so they no longer ask you for missions (game effect is locking that team which the AI can do too).
To be fixed
By forming an alliance all your allies should be set to peace and if they break that then it pops up a decision box asking which side you wish to support (degrades the relation with the other). By not having to supporting anyone, it is very unrealistic right now. You should also have the option to influence peace and diplomatic relations between two races, so that you can form larger alliances (AI's too).
Currency, by its very definition, is not a commodity.
That's enough (for now...)