I'd like to see many more planet types. That's pretty much a must, I simply don't play vanilla SoaSE Entrenchementany longer because more planet types is more munner, the mods make it better.
It would be interesting if Pirates went after trade ships not planets, and if they ran away a lot when big fleets showed up. They've no reason to fight to the end, they should just jump to a different planet and steal more stuff, perhaps make them a tad faster.
Let you sell ships on the black market. You would get a lot of money (ie more than you spend on making the ship, but you wouldn't have control over who bought it, could even be Pirates... You could sell ANYTHING on the black market, even Capital ships, and so could other nations. You might even occasionaly be able to buy a ship from a different faction, you couldn't upgrade them however if htey're from a different type of tech.
Trade: A planets output should be based on it's culture and the ammount of resources available to it. You should be able to set up resource trading that sends resources such as Metals, Crystals, Antimatter, and Food to planets deeper within your empire. Food would allow you to grow a planets population to enormous hive like levels (think Coruscant from Star Wars), a planets speed of production should be based on how much of a particular product is avaialble to it, not to the overall pool of resources.
Resources should be pooled, ie you should be ablee to attack places where they're pooled, rather than they be "off the table". You can build resource stores in orbit which are limited, but can be moved between planets (albeit somehwat slowly) or you can store resources on a planet (which can't be moved as quickly, but must be spent on projects in THAT gravity well). Moving resources between wells is possible, requires trade or mining ships, and there is a loss in the resources aboard each ship per gravity well it visits while going to the overall storage. Resources would be limited on planets based on the overall population of that planet and or Starbases in that well.
This makes it cheaper to put factories that build ships in places that are close to areas with high resources, It makes certain planets and g-wells much better targets than others (eg you attack a well and take all the resources based there for your self, this would also make areas for pirates to attack)
Higher populations would result in higher tax income, but after a certain point, those planets with very high populations would be dependant on planets producing an excess in food. It would be a lot of fun to conquer the high population planet's food supply and give them an ultimatum "Surrender or Starve!"
Several new construction types
Antimatter Factories (several sizes), these would blow up in increasingly impressive levels, with the larger ones potentially depopulation the gravwell they're in, and destroying most ships and structures, perhaps even shutting down phase lanes to that well for a few minutes of game time. Antimatter facilities would perform best in wells arround stars (and would be buildable arround them naturally).
Orbital Living Quarters (expensive, but they increase the planets overall population, these would go from small stations to enormous facilities holding buildings of citizens),
Resource Storage Facilities (raise a planets Resource storage levels, allowign it to build larger projects),
Greenhouse Facilities (these would make food, either for the well they are in, or to be traded to other planets in order to increase those planets population capacity. These would have a boost or penalty to their output based on the type of planet they orbit.
Currently conquering a planet merely reduces the overall pool of resources avaialbe to an enemy empire. Makign it so that a mining planet near a factory planet is more important than on on the other side of the empire will make the game more strategic. Allowing us to increase populations using orbital housing and shipping food from other planets (Terran being the best at creating food) make Terran planets very valauble, centers of fighting)
Making some factories like Antimatter factories capable of causing damage to the well or even Phase lanes passing through it make the use of Antimatter factories both useful (they would boost AM production in ships near them, reduced per well the AM is "passed" through.) but risky (you could poossibly kill one of your own planets or even trap your fleet away from retreat or reinforcement for a few minutes.
International trade: This should be more specific. Eg you should be able to ask or be asked to trade a specific resource and quantity of it from a specific gravity well at a specific cost in resources or money from another well.For instance: The TEC asks the Advent to trade 2 food units food from Planet A (Adventian controlled) to Planet T (TEC controlled) in return for 2 Crystal Units from Planet S (TEC controlled) to planet B (Advent controlled)
Trade skill This is a technology you research, you gain a bonus in what you get from international trade with this. For instance TEC is trade skill 2, they gain 20% over trade policies with other nations, the previous example would result in the TEC getting 2.4 food from the Advent (the Advent woudl still get 2 Crystal) Naturally the TEC would be best at this.
...Just some ideas and finetuning previous ones.