I think the pirates in this game could be much more complex and fun. I'm just going to provide a lot of theoretical scenarios that could play out in a game that I think would make the pirates more interesting and fun. One thing I will mention is that I'm working under the assumption that instead of the current system where there are just "pirates", there are now different pirate factions.

A large pirate fleet has arrived at one of your planets and you probably won't be able to fight them off. Since they are pirates, all they want is to pillage your planet for money and other resources. You contact the pirate fleet's leader and offer them a sum of money, resources, ships, or something else to leave you alone.

Two pirate factions are fighting each other in one of your planet's gravity wells. You have a number of options. You can stand back and wait to see who wins, then destroy the survivors. You can contact one of the fleets and make an agreement that you will help them destroy the other faction in exchange for them to withdraw from your territory after the fight, or perhaps in exchange for resources.

You are contacted by a pirate leader who wants to buy safe passage in your territory from you. This will increase your resource income, but they probably want this so they had hide from some other faction. Expect an increase in pirate attacks from other factions.

You are contacted by a pirate leader who is planning a raid on a planet owned by a rival empire. They are asking you for money to fund more ships for this raid. Since all they want is to destroy it and loot the wreckage, it will then be left empty for you to move in and colonize. The more money you give them, the larger the fleet they attack with is.

You want to attack an allied planet without going to war with them? How about paying a pirate faction to make one of your fleets look like theirs. If all goes well, your allies will think they are just being attacked by pirates. They might figure out it's you, though, and then everyone in the galaxy will know how much of a devious evil bastard you are.

I will probably think of more later, I'll post them if I do.