Paradox put no effort into the game at all. Imperator Rome functions a lot more like what Stellaris should have.
They should have made it possible to change Ethos from the start, but instead they waited forever to do that. Sectors ought to be like vassals which are directly controllable have sectoral governments, the type of which can be chosen (like imperial appointed viceroys, federal states, etc.). If a sector is old enough and/or has a strong enough political identity (ie, shared faction/ideology predominates on most of its worlds) and/or a strong enough ethnic identity (common species), then the sector should be able to spawn in the equivalent of cores in other Paradox games, representing a nascent nationalism. Alternatively, we could imagine that pops might have a "Nationalism" identifier that represents the state that they want to align with (which by default is the one of their parent pop that spawned them), and sectoral nationalism can introduce new ones, so you have issues both with assimilating conquered/immigrant Pops and with your own species fracturing into regional identities as the colonies become more established. Sector size management should be a factor where sectors can overextend like their parent states, but you also have limited ability to manage multiple sectors (like vassal limits), and fractured sectors are more demanding in that sense but also less politically threatening. Whatever sector the capital is in should always be regarded as the cosmopolitan/"state" sector, like a primary culture/crown land.
When a sectoral government is angry enough and has enough of a power base behind it it should be able to launch a civil war to seize the government or (if it has cores) for independence. If one rebellion breaks out, it should make other sectors more confident to rebel, even if they weren't that eager to; conversely, loyal sectors should bolster support for the government, and neutrals potentially negotiate for concessions to both sides. When sectors rebel, they should be able to recall their supporters, resulting in them spawning in armies and having subsidized ship construction, along with shitty ships spawned. (Might even have something like sectoral militias that act like a cheap reserve, but pose a threat in times of unrest) while penalizing the loyalist regime's forces temporarily (representing understaffed armies and ships before defectors can replace them). Fortifications and ships stationed in sectoral harbors can flip or not, representing struggles to violently or nonviolently seize installations in preparation for war. Officers can defect and military defections and the presence of things like War Academies (or whatever Stellaris calls them, I think there's some building like that) should have disproportionate effects.
This is really separate from the political aspect, but I think Stellaris' army system is the laziest, shittiest thing I've ever seen. The Paradox fanbase didn't care because they said sci-fi isn't about armies, which is ridiculous, most science fiction focuses on land combat (iconic things like the Droids and Clones and Jedi in Star Wars, or Starship Troopers, or other such). I don't know how you'd change it when there's no maneuver, other than maybe through representing some kind of maneuver on the surface or combat events where you make strategic decisions. Conquering a planet ought to feel like an achievement. Fleets ought to have a representation of manpower. Although classic space operas don't represent this - space travel is really casual in them - any warship is basically going to be staffed by a ton of the best engineers and scientists available. I would imagine even people like the lowliest astronauts on warships would be the equivalent of both military officers and graduate students. In real-life space opera I'd think that the real cost of space warfare wouldn't be raw materials, which are trivial, but extremely expensive (in monetary terms) machining of the ships and the servicemen who would take much longer to replace. Navies would be terrified of losing ships less because they'd lose ships and more because they'd lose a generation of experts. Sailors in the Age of Sail were actually like a less extreme version of this - a highly-skilled workforce that served as a practical constraint on navies - and Paradox tried to represent that in EU4, but they fucked it up by making it a trivial mechanic and having galleys take up more sailors than sailing ships, which is accurate in the sense that galleys had more hands, but inaccurate in the sense that galley sailors were low-skilled mongs who could be easily replaced, Mediterranean sailing fleets were massive in part for that reason whereas Atlantic fleets were tiny.
Oh, it also could have used some attempt at a trade system and markets. For example, the Investment Pool in Victoria III is brilliant. Instead of having market economies be "command economy but extra Energy," have it be that you have different pools with different restrictions. If you go Collectivist, you have lower efficiency (unless you're something like a Hive Mind) but you get to expropriate more of your investments, so you have lower growth potential but can pour more of it into non-consumerist goals. If you go Individualist, you get high efficiency but less choice. Those should have been split up anyways, what it tries to convey with Individualist vs Collectivist is a combination of Authoritarian vs Democratic, Totalitarian vs Liberal, and a sort of cosmopolitanism vs traditionalism that's kind of represented by Materialism vs Spiritualism and Xenophilia vs Xenophobia. Energy credits are a sci-fi staple but a retarded one: the ideal means of exchange is something that can actually be stored up and is not consumed. It should have just had the alternative cliche of generic credits, something like a world of cryptocurrencies. Energy should be something which is more like an infrastructure limit on a world, like how many nuclear plants, hydro-dams, solar farms, etc. you've got running, with the possibility of exceeding local limits by doing things like important uranium (so you can exceed local mining rates). For planets to export and import would require a Merchant Marine, which demands Space Elevator/Harbor/Shipyard infrastructure to service, maintain it, and expand on it. Heavy Merchant Marine presence and low military presence would dynamically incentivize piracy. I think it'd be great if Minerals were split into common and rare ones, Electronics added as an advanced resource (used in other advanced resources) made from the rare minerals, Spaceship Parts added on top of that, and Pops working in "Astronaut" and "Space Force" jobs that contribute to a slowly-replenishing pool of astronauts (be fun if you could have Space War of 1812 over space-impressment) to crew the ships.
I think it would have been cool if Mining Stations were little one-Pop colonies that are captured in warfare.