I was thinking of developing something along these lines as well (read: thought it would be cool to do so but never had the time to do it actually :D), so I will post compatible ideas.
The emperor resides on the throne planet and can't move. Instead he has 3 henchmen of unquestionable loyalty which can be moved around and act as extension of emperor's will.
There are several special units, like imperial guard that can't be moved from the imperial palace, various spies, imperial inspectors, etc. You either can't build these units or there are high limits.
You can't create fleets. Instead you have 12 nobles (actually 10 nobles and 2 imperial admirals), each has his own fleet. You can give ships to a noble and it will be included in his fleet. Fleets can never be split, also it is easy to add to fleet but hard to remove from it :D You can move these fleets around and these basicly do what you told them to do but the actual effect depends on the fleet commander. And of course nobles and fleets can rebel from time to time
Or be unavailable because the commanders is preoccupied with some other thing. The 2 imperial fleets (commanded by your imperial admials) are always loyal and not troublesome, but these admirals are not necessarily as bright as nobles plus nobles will riot if the imperial fleet is too strong compared to noble fleets.
Each planet has planetary forces (ground army). These armies can not be moved from the planet. You can enforce planetary garrisons if you wish. You also have several imperial infantry regiments which you can move between planets.
Finances. You build all ships yourself and these are moved to shipyards when finished, then you add these to different fleets. But the maintenance of ships is done by the commander, which means you pay for maintenance of imperial fleets but noble fleets are maintained by nobles from their treasuries. Nobles have very simple income system (% of income from their home planets goes to their treasury). If the noble has not enough money he is very displeased (and take a loan from banking guild) which in a long run leads to noble's revolt. Some nobles are more wasteful than others, they can crash their treasuries by spending on luxuries. Some also are richer than others (so you can't really give more ships to a poor noble even if he is loyal and competent because the maintenance will kill him).
You have several imperial offices, these can be given to nobles (the same that command fleets). This increases their happiness and sometimes income. Of course it would be best to not give offices to nobles with "corrupt" trait or "unjust" or "cruel" because it damages the overall empire.
I was thinking if maybe making more nobles per noble house would be better? Like the commandeing noble is one and you have additional 2 nobles from the same noble house which can be granted an office (hoping one of them is half decent nad not totally insane) which increases the loyalty and happiness of the whole noble house.
You can dispose of a noble if you really want (replacing it by another randomly generated noble from the same noble branch), but it causes a big drop of happiness among all noble houses ("the emperor is trying to claim all the power and make us his puppets").
Assasination is fine, but don't make it "kill the emperor" but save the emperor making him only injured, like 50% command points for 10 turns, or kill some courtier instead (bravely protected the emperor with his own life).