First a picture to get you into the mood :)
You are the Emperor, let's say it's a late game and the empire has 200 planets, so your personnel consist of 200 planetary governors, 202 army officers (200 colonels responsible for defending a particular planet and 2 generals), around 50-150 fleet officers (5-9 fleet admirals and 40-150 squadron commaders) plus like 20-30 special officials (ministers, courtiers, ambassadors, inspectors, etc). So we are taking here about 500+ NPCs.
Question is, how to manage them?
Obviously the traditional "select who should do what" won't work here at all (you can have it if you have a game like MoO2 with 4 or 8 "heroes"), the player's mind would overload :)
How it works at them moment. At the end of turn the game spawns an official for every unoccupied spot (no player's choice). All the player can do is fire am official (and then the post will be unoccupied for this turn and new one will arrive next turn, which mighht be worse or better, completely random). I would say it's not that that bad in practice (I put it as a temporary quick system, but surprisingly it has some charm to it, it allows to make decisions without mind meld and gives the impression of an Emperor of a vast empire who don't have the time to control everything yet can get rid of the incompetence).
Now to dig deeper, originally I planned that every planet has like 6 local politicians and the player chooses who should be the governor (so the choice would be restricted to those 6 only). So you don't have a long list of hundreds of NPCs and you thinking whom to put to what position. Yet, I'm not sure if the current system "the court chooses the gevornor for each planet and the Emperor can only order replacing a governor" would not be better...
Another thing is military, the Emperor dwelling into low level internal affairs of military (like who commands which squadron) is not so good. The Emperor should have a lot of saying about the Admiral position but that's it. Squad commanders is not what Emperor appoints, it just feels wrong... A quick solution here I thout of is 2 options (separate for each fleet) "replace admiral" and "replace all officers in the fleet". As for army I have no clue at all.
Imperial court. Court would be a group of people who more directly help the Emperor, a sort of central government. My idea here is that upon audience you are allowed to "promote" any governor (only governors, no military officials) to the court. Such governor vacants the planetary post and moves to the imperial court (I think there would be like 12 Courtiers slots so they would look like in the audience picture above). You can not demote courtier to a governor position, only fire permanently. Maybe you would be assigning them tasts to do (sort of like "ministers").
Ambassadors - dunno.
Note: I'm especially looking for ideas about military officials.