Pirates should have fast, but weak ships. They should raid traders and for every trader they raid, they get more money. They can also get money from destroying other ships, but they get the most from traders.
With that money, they can upgrade their ships. Pirates actually have access to all technologies that at least 2 civs have (like the barbarians in Civ).
Pirates can upgrade and buy ships, with the money they get from raiding.
Eventually pirates could get so powerful or wealthy, that civs would find themselves incapable of playing the game, without making peace with the pirates, which requires a monthly tribute.
So pirates are initially a small problem, but gradually grow bigger and bigger if left alone.
This sounds like a good idea. Pirates fighting all-out with big, interstellar fleets don't make sense to me. They should just raid freighters in certain routes and run away with their fast ships. Your defense fleets arrive ten weeks later, with no pirates in sight.
And as for who would support the Space Pirates... think, who supported the Pirates in the Age of Discovery? Governaments. The English, the French and the Dutch were pretty pissed off that they didn't take part on the division of South America between Spain and Portugal, so they started raiding ships, mainly those ships full of silver coming from Spanish America.
Pirates should't be just a neutral force who attack everyone (Although some real pirates were like that, most were actually privateers), they should be small bands who can be hired by governaments with influence and shady contacts in outer, poorer colonies. Bringing economic ruin to your enemies by paying a group of Space Privateers to raid their trade routes seems to be a interesting option for me.
I wish there were food freights like in MOO2. That would certainly make Privateers even more frightening, capable of starving whole planets.
