Let me preface the whole thing by saying: That I don't mind pirates being an active part of the game. However I feel like their purpose being primarly an early game nuisance. As it stands they are little more than an aggressive separatist faction. They lack actual pirate character so to speak.
So here's my idea:
- have separatists actually exist in a game as scale of your system's morale, have them act like pirates do right now
- have pirates still infesting ship junkyards
- in times of peace pirates should primarily focus on disrupting resource and local cash flow as well as any trade, in times of war have them act as privateers