Colony ships and transports
When you load up a transport or colony ship. Instead of removing the population of the planet, it leaves them in place but do not pay taxes or anything like that but do eat food. As soon a new planet is colonised, all the citizens are removed and added to the new planet. Transports would have to be sent home with the soldiers on board after an invasion to get the people back. This way you would not be able to continually load more people onto transports, in order to "make" more people and create a vast invasion force over time.
Destroying a colony ship, should only be available as an option to a very evil civilizations. Such ships should not fight in battles, but should be captured.
When you capture a colony ship you would be able to enslave it, or turn it back. Enslaving it would allow you to send the colony ship to one of your worlds and add them to the population as slaves. This would be an evil option.
Turning it back, would forcibly send the colony ship on auto-pilot back to it's original world, where it is then automaticly destroyed, assume that the attackers have hacked the ships computer, rigged the ship with explosives and so on, in order to ensure that it returns to it's homeworld and then blows up.
A transport also follows the same rules.
Instead of merely destroying them, you should have the option to loot a freighter. You get all the value of the trade route, in the time it would take to get between the worlds and the freighter counts as destroyed. Looting freighters is the princal source of income for space pirates (see below)
Constructors can be captured and then used to build or improve the capturing civilizations starbases.
Space Pirates and their bases
Space Pirates raid freighters and loot them to gain income. That is their only source of income, income which they then use to buy new ships at their pirate bases.
Pirates recieve the technologies of all the civilizations in the game, as regards ships and design new ships like any other player. Pirates tend to favor speed, range and sensors over firepower though. They are cowardly and typically like to attack freighters and then outrun any forces sent to get them.
There would be a number of pirate bases scattered throughout the galaxy, in uninhabited systems and they are located on a class 0 planet. These bases a located as soon as the technology trade is discovered by a civilization. New bases are placed by event througout the game, to replace ones that have been destroyed/
Bases allow pirates to buy new ships in their bases, for exactly the same cost that would cost a civilization to buy that ship.
Space pirate events, give the pirate faction, a lot of money that they then use to buy fleets of pirate ships in their bases, which can then be increased by stealing money from freighters.
Bases are ordinerily invisable and any pirate ships in bases are also invisible. The way to discover a pirate base, is to observe a ship leaving or entering a pirate base. The Pirate AI, should be reluctant to do so however, if there are ships it can see within sensor range of the base. The best way to discover pirate bases, it therefore to have a very sensor heavy ship, to scan worlds that you suspect as harbouring pirate bases.
Pirates should buy sensor ships of their own however, which would act as lookouts in orbit around bases, these act to detect ships that might be spying on them. A well funded pirate AIs bases, would have highly advanced lookout ships, so depriving a pirate player of funds should be key to eventually finding their bases.
Once discovered, a new very powerful ship, armed and protected to the maximum level available to the pirates, is located in orbit around the planet. This is the pirate base ship. If you attack this ship, then the pirate player is aware of it's being caught and then ship will then leave orbit.
The pirate base ship, will wander about until it finds a safe unwatched unihabited planet, to set up a new base in. It can raid freighters and the like on the way though.