This has probably been suggested over and over again, but I'd like to see pirates added to the game. It'd be a good way to encourage players to invest in their military early on before they've actually encountered any NPRs and act as a 'tutorial' of sorts for combat before players go on to have proper battles.
Pirates should be weak, but annoying if not proactively dealt with. Early on you should be able to defeat them even with PD weapons as their first crafts will be barely large enough to mount a small boarding bay and an engine.
By acting as a low-risk enemy, it will get the player thinking about tactics and strategy in Aurora a lot earlier, which is good because a lot of people I know (including me) can count the amount of times we've been in combat on one hand since we always restart before getting that far.
Their designs for each component should always be at least 3 tech levels below anything you have researched AND DEVELOPED (pirates won't do their own R&D) UNLESS they mange to board and capture one of your ships. Then they have access to the technology present in that ship's components. So keep your big ships safe!
The pirate AI should obviously focus on boarding and capturing ships above all. This is vital for them, as pirates start out only being able to build 1000-ton ships from scratch. However, they can convert captured civilian ships of any size into military ships by overclocking the civilian engines and strapping on some guns back at their base (more on this later). This means a pirate that captures a 50,000 ton civilian cargo ship (a staple of my games) now has 50,000 tons of space to convert into a warship. Scary!
However, there are obvious drawbacks to converting a freighter to a battleship. One is that every component has increased maintenance requirements. Another is that engines and armor can only be boosted by so much. A fledgling Pirate Hideout on a rock somewhere won't be able to slap on more than 1 layer of improvised armor or boost civilian engines past 75%. A Pirate Haven however...
This brings me to the next important thing you have to know about pirates; their outposts. Once civilians have spawned, pirates will also start to spawn to raid them from their bases. The bases will never spawn on planets, as those are too conspicuous and interesting for the authorities, but rather on asteroids and small moons that would generally be undesirable for colonization and well away from other populations. Pirate Bases start with a Deep Space Tracking station (3 techs below yours), a military shipyard locked at 1,000 tons, an ordinance and fighter factory, and some maintenance facilities.
Every prize it takes is taken back to the base, where its cargo is converted into wealth (divided by 3) and is either itself sold for its wealth value (again divided by 3) or converted into a pirate vessel. As a Pirate Base gains more and more wealth, it will expand its fleet and increase the capacity of its military shipyard. It can also add more layers of armor to salvaged commercial ships, boost commercial engines higher, and lessens the maintenance penalty for commercials converted to military. Garrisons and even STO's start to spawn, and larger Pirate Bases can smuggle advanced tech to close the gap between you and them until you are on par with one-another. If you let a base flourish, you could soon encounter a fleet of home-made pirate ships that aren't total pushovers in the face of a proper navy.
Pirates will ideally set up in systems with no populations or naval presence, but a lot of civilian traffic. Having a colony won't deter them however, especially if its a new colony with only a couple million people. Stationing a big enough naval force in the region will suppress pirates from spawning to a large extent, and Pirates won't spawn on bodies where they will be detected by sensors. You can also starve them by keeping them from taking prizes, as they have bills to pay just like everyone else. If they go too far into the red, they disband. Pirates will capture crew and colonists to grow their population, which they put to work in the shipyard, making civilian goods, or mining if minerals are present. A larger portion of the population can go towards these efforts on Pirate bases, but that comes with a larger attrition rate. Unscrupulous civilians will actually turn off their transponder to trade with pirates discreetly, giving Pirates an alternative way to earn income.
A Pirate faction's endgame is to seize a colony close by and declare themselves independent, at which point they become a normal NPR.
More NPC controlled organizations like these will really give your Empire more life as well as a chance to gain experience in a part of the game that many players fail to get to in a lot of playthroughs.