Is it currently possible to raid or blockade trade routes? If it is, then pirates should definitely do that. And privateers would be a very welcome addition.
Also, I agree that there should be separatists on your low morale colonies. But if they succeed in separating, I don't want them to become a generic "rebel" faction. They should become a major (or maybe minor) with their own name and leader. Essentially a new fresh faction added in the middle of the game.