Since the rebel topic got somewhat sidetracked by negotiations, talking, being a nice emperor, etc, let's first talk pirates :) No negotiations, no ethics. You just need to eradicate the scum and that's the right and the only way to deal with them (and no, don't even try suggesting to hire them or something similar, I want a pure bloodshed in this topic) :)
Typically pirates are implemented in a completely nonsense way: there is a base of pirates, they are super strong and the player fears them, then the player gets stronger, eradicates pirates in one battle and there is no more pirates ever again. Total, utter nonsense :D We need to fix it.
First, pirates want profit, so they don't want to fight the player's fleet (even if they are stronger), they want to pry on unarmed merchants or pillage planets without defences and demand tribute "or else" from small colonies. Second, you can't get rid of pirates, there is always someone new thinking it's a good career path, so if you destroy pirates completely, after a longer/shorter while there should be new pirates (same with bases, these definitely can pop up again after being destroyed or something).
Ideas how exactly it should work?