So, there is a space empire. It is lead by the emperor (the player) and there are several noble houses (AI controlled). There are also hostile aliens surrounding the empire. There is a sort of balance of power between the emperor and the noble houses (on one hand they dislike themselves on the other they need each other).

How this system evolved (politically)? Why the society formed this way? What's so special about the noble cast that they got the power in a sci-fi setting (but I prefer to not focus on technology here)? Is there a parliament of some sort? How the economy works? Are the people serfs or free man? Are there corporations or the whole economy is nobles controlled? Or guilds maybe? Also, feel free to post about anything related it's a very loose thread

The desired mood is a bit feudal/medieval like (but a bit, very loosely). For example, bonus points if nobles got power because of genetics ("noble born" :D).

Maybe the nobles control some resource that the empire needs but can't easily replicate or take by force.

Take for example the navigators in the Dune universe - due to their spice-induced mutation they're the only ones able to safely allow FTL travel, putting them in a position of power - War Hammer's Navigators work with a very similar principal, being born with a special gene.  Likewise in the Dune setting, the house controlling the planet Arrakis controls the supply of spice which even the navigators require, again putting them in a position of power.

I don't know many details of your setting, but if there are any similar resources or technologies available in your setting perhaps the noble houses control them.  In the case of something like the mutation of Dune's navigators, you might have the genetic tie-in you were after.

A couple of technologies they might possibly control are FTL travel, fast communications, and manufacturing capabilities.

Alternatively, maybe the noble houses defend the empire against the hostile aliens.  The noble houses stay in the empire for the additional resources and trade opportunities it affords them, while the empire allows them to maintain some independence to save spending more government resources keeping the aliens at bay.