On pirates: I'm hoping this would couple in with a "domestic unrest" system, i.e. rebellious planets, economically oppressed planets, etc. One way to do this might be through gunboats (or even fighters) rather than full-up ships. I forget how hard it is to detect GB bases on a planet, but if it isn't an autodetect situation, then they could pop up on poorly-governed worlds in the same way civilian space centers do. Or a civilian cargo ship could drop a GB base off on a nearby asteroid or moon, and regularly perform re-supply runs. Or the cargo hold on a civilian ship might actually be a hangar bay for fighters. The core idea here is that piracy would be a function of lawless populations, and could actually be based on worlds controlled by the empire. One nice part of this is that it gives a motivation for having armed fleet units (and security/military units?) even if no external threats to the empire (NPR races) are present - they would be needed for piracy suppression. It could also change the garrison requirements from being hard-wired to being a decision made by players: pirate attacks would increase unhappiness (leading to lower productivity); ground forces would reduce lawlessness (reducing the chance of pirates springing up) while naval patrols would provide protection.
This model also works for "privateers" or "freedom fighters" - a conquered population might have a high chance of producing "pirate" (actually rebel) bases, while another government might spontaneously commission civilian Q-ships. The lawlessness and/or pirate/privateer probability could also be skewed by government type.
I don't have detailed knowledge of it, but my recollection is that the vast majority of historical pirates didn't have a blue-water capability; instead they were short-ranged boats full of men which preyed on coastal traffic. This seems to be what's been going on off Somalia until recently, and also the sort of pirates that have been active in Indonesia (Straights of Malacca, IIRC) for many years now. It seems like the Somalian pirates have recently gained blue-water capability by using "tenders"; this is where the idea above for civilian cargo ships that actually have hangar space for GB or fighters came from. Another observation here is that, in both cases, they're operating near choke points or navigational obstructions - the Aurora equivalent would be to find an asteroid near a heavily used asteroid and park a pirate base there.
John