First off, espionage: Maybe I'm missing something, but espionage really needs some other way to plant spies without having to hurt the recipient.
Plant spies in planet capitol or non-usable tiles for information gathering: Planet capitol wouldn't stop working. Spies placed in this way would gather more intel then their sabotaging bretheren, and the AI would rarely nullify them.
Or
Place spies on planets but not in tiles: This would require some special buttons. Spies placed in this way would gather more intel, wouldn't sabotage anything, and would be invisible normally in planet views and the espionage tab.
Security Sweep special espionage command to root out hidden spies: Initiating a security sweep would temporarily use all unassigned spies. It would last a number of turns equal to the total number of planets the player has, divided by the number of spies being used for the sweep. It would cost a certain amount of cash per spie used. At the end of the sweep, all hidden foreign spies would show up normally in the espionage tab.
The ability to give spies more than just saboatge jobs would be nice. Focus them on stealing tech, or have them siphon off tax income. Plant spies in shipyards to sabotage ships produced there, dropping their base HP slightly.
UI improvements:
Planet improvement templates would be really nice. Once you get past 20 planets or so it becomes a real pain in the heiney to make sure all your planets have the standard improvements you want. Quality bonuses, new improvements, rebuilding a planet recently taken from the AI.
Just a simple UI construction list and a button on planets to apply it. In the list, options to prioritize certain improvements going to certain tiles. Like a factory could be given high priority for manufacturing tiles, and Do Not Build for research, food, morale, and influence.
Also, options for tearing down imrpovements already on the planet that aren't on the list (do nothing, replace as needed, tear down all), and wether to ignore special improvements (the one per planet ones and the like) when deciding wether to tear down or not.
A way to send an upgrade order to all ships of the same type, like you can with fleets, would be nice. Instead of going through 80 worlds and upgrading the defending ships to the latest version one by one it could be nice and quick. Include an option to have it upgrade as many as it can with the current financing plan, instead of just all or nothing.
Starbases: Habitation bases, Travel bases, Total Terror-former, Dyson Spheres
Habitation Bases: Either as a stand alone starbase, or an option for use on the 0 habitability planets. The first constructor used would create a station with a habitability of 1 and population cap of 0.25 billion. Each new addon would add 1 more habitability and 0.25bil pop cap. Adding a module would require a couple week construction time. Create a new value per race that dictates the max number of habitat modules capable of being added, starting at 3 or 5 and upgradable via tech researches.
This would be a starbase type, like economy, influence, and military. The standard battlestations and weapons would be valid choices.
In case of an invasion attempt, have a special battle where only the first round of combat is determined. Any troop ships killed would be gone from the invasion, any surviving would reduce their troop counts by the ratio of damage vs max HP they took (if a troop carrier takes 7 damage, has a max HP of 21, and carries 1000 troops, drop the troops remaining by 7/21, 1/3rd).
Travel Bases: Travel bases, once built, must be given a destination. When a ship enters a travel base it enters auto-pilot towards the destination point and gains a large movement bonus. Canceling the autopilot would cancel the movement bonus too.
Travelbase specific upgrades would include larger movement bonuses, sensors to give view of the destination point, life support upgrades to give a small life support area around the destination point, and a final movement tech that would create a stable one-way wormhole between the base and it's destination.
Total Terror-former: Like a Terror base, the Terror-former would be a super base project. Taking multiple constructors, many weeks of build time after all pieces were upgraded, and having a very small movement rate. The resulting ship/base would be able to target planets instead of stars, and instead of destroying them outright, it would destroy the planet, everything within 1 or 2 squares, and be replaced by a new planet with a medium level quality, boostable by tech research.
Usable on empty planets and colonized ones alive, it could be used to either boost the number of habitable planets, or be used as an unstoppable superweapon that wipes planets clean of all life.
Yes it's based off of genesis.
Dyson Spheres: Another large superbase project, this one takes a star and completely surrounds it with a habitation sphere, absorbing all it's energy output.
One the plus side, it creates a planet with a maxed out habitability. On the downside it permanently drops the habitability of all orbiting planets to 0. Planet quality effecting tech and improvements have no effect on this.
Misc: Ideas that don't fit with the above catagories.
Good, neutral, evil decisions: For the love of god, why are the all along the lines of "Evil shall triumph cause good is dumb".
Take the Stripmine the protected park one. Good gets nothing for creating a beautiful, protected parkland, neutral gets a small bc bonus, and evil gets a sizable one. Why? A beautiful stretch of parkland should give a small moral boost.
And the Refugees ones, evil gets a production boost, while good loses a lot of cash.
Balance them out, give good choices bonuses that don't directly effect cash reserves, military might, or production. Morale, diplomacy, influence, ect... boosts.
I've noticed that once you pick an ethical allignment, no mnore choices pop up. Again, why?
Have it so they still show up, but effect race wide moral. A choice 1 allignment away (good/evil to neutral, neutral to good or evil) apply a 1% moral penalty, and if the choice is 2 away (good to evil and evil to good), apply a 2% penalty.
Players could negate the penalty by balancing it out, each choice made al their own allignment would negate a 1% penalty (so it would take a good player 2 acts of kindness to negate 1 evil choice).
Would only really work if the choices became balanced more, cause as it stands an evil or neutral player would never choose a good choice.
Ship improvement, Chaotic Wormhole Generator: A movement upgrade for ships, it would be a fleet wide thing. When activated, it would teleport the entire fleet to a random location. Useful as a last ditch way toevade persuers, or for scouting.