Could pirates use regular non-subspace subspace engines to leave a starsystem and hide outside it? Would they need to?
I usually imagine one or possibly two planets as major places. Maybe some anti-orbital cannons on the surface (definantly not for attacking fighters, but probably very powerful turrets designed to bring down destroyers that are launching fighters and transports at the planet's surface). Maybe one installation the is in charge of defense of the planet, and that houses civilians. This station is the police base or something, and the fighter squadrons probably fly (at the time of fs2) Myrmidons or Ulysses. Cruisers and fighters patrol in low orbit around the planet (lower, and medium, probably older Leviathan and Fenris cruisers). Civvy ships exit orbit and must leave the planet's gravitational field before they jump (or at least get where it is weaker). Civvies are free to roam around the system at their own risk, but in most core systems, I think pirate activity would be low.
As for military fleets, station is near enough to the jump into the system that it can protect it, but far enough that something coming through will have a chance at being stopped before it hits HQ. I would imagine they aren't built extremely close to planets, to prevent the GTVA from losing both the station and the planet, but close enough to be able to effectively protect the planet.
EDIT: As for government. Terrans, I see a government very close to US democracy (seeing as the creators of the game were from the US). The Vasudans seem to thrive under an emperor better (Khonsu II helped them out a lot, but he abolished the parliamentary part of PVE) I assume that the emperor has more power than a prime minister or president, but a general assembly or congress has the power to make sure he doesn't become to powerful. I don't think there would be an issue with the next emperor being in the same bloodline, but I have no evidence to support that claim. I think the emperor is probably chosen in a similiar way as the pope. The people (maybe, not sure if the people do it though) choose a few likely candidates and a group of advisors (referring back to the pope, like Cardinals) select the new emperor. Often an emperor's son is chosen as the new emperor, to honor that tradition. The new emperor rules until he dies or resigns.
Just my two cents...