Ape Apps

Resources are classified into 3 types: Yields, Special Commodites and Strategic Resources.

• Yields
  They are resource outputs from any city and colony. Among the Yields, Supplies is for population growth, Industry determines how fast the city/colony can produce, Research contributes to technological development progress, Income adds money to your national treasury, Energy powers local special facilities. Except money, other yields are not stockpiled - only has supply and demand.
• Special Commodities
  They are rare but vital resource for maintaining obedience of your civilization as well as valuable commodities for trade and boosting economy. Like yield, they are not stockpiled, and only has supply and demand. Examples such as Spices from My Starship and Marbles can only be extracted from available deposits, but things like Rum and Arts does not come from deposits but specific buildings (that are available for any cities and colonies).
• Strategic Resources
  They are vital resources for building some advanced structures, and especially, building up your military. Strategic resources in my mind so far are Titanium (advanced metal), Uranium (fuel), Crystalline (advanced electronics raw material), Ether (advanced chemical) and Triantanium (super alloy). They are the only type of resources that can be stockpiled, and only accessible from extracting corresponding deposits in the system.

I think the research gameplay would be more or less the same as the one in My Empire. For a common or a different tech tree between different factions, it is up to your consideration and decision.

Of course, most battles involved would be space battles. But let's make battles on planetary surfaces also count - The planet is only "captured" after winning the land battle or the blockade is long enough for the local forces to surrender. The system can have local defensive forces on land (e.g. militias), and there are some starships that are specially designed for landing warfare (e.g. dropships).

Next idea. Space vessels, no matter civilian vessels like colony ship or military vessels even the lightest frigate, can only operate in limited range where logistics are available. These operation range are normally provided by colonized systems, but if you need a further reach, you can build space stations - which serve as logistics depot that expands operation range as well as a defense station that can repel small scale offensives.

Political territory decides what are yours, what are others' properties, and what are neutral. You can only extract resources in your political territory, and relatively, other civilizations normally cannot have access to what inside your territory. These entities provides political territories - Space Stations, Colonies and Cities. Colonies provides relatively weaker political influence.

As always for a civilization sim - diplomacy has its importance. Good diplomacy opens opportunities and allows you having access to some exotic resources (without using "much" violence), as well as establishing some reliable alliances that protects you from potential foreign threats.
Diplomacy with minor civilizations would be very simple. A good relations opens up trade with them, a better relation turns them into puppet state members of your great empire. Of course, a bad diplomacy with these smaller empires still have some consequences, militaristic minor civilizations may even invade your empire with their own fleet.

Although the word describing it might not be accurate, but generally..... public order, morale and happiness. Each system politically belongs to yours will have a rating of obedience, which impacts battles occurring and yields in the corresponding system. Luxuries, social infrastructures and presence of some defensive troops with martial law trait (e.g. United Earth's Security Forces) generates and adds obedience. Enemy blockades, sabotages, losing battle and overcrowding are major factors decreasing local obedience.

If a enemy blockade takes place, when obedience dropped to certain level, the local government surrenders to the blockade enforcing civilization.

Using your fleet to blockade your own planets does also lower obedience, but the obedience value is maintained to at least certain level. When things have gone far worse, using the might of your fleet can restore some public order.

Not considering wartime situations, if local obedience dropped to 0, it would become renegade city state, attempting to break off from your civilization.

Capturing an enemy system will always decrease the obedience of the captured system, but would never drop beyond certain level (which if the value is lower than the limit when the system is captured, the obedience would instead increase to minimal value).