Natural Diversity: Millions of years ago when your species was still young, geological upheavals divided your world into several isolated regions, creating a vastly diverse array of traits within the various populations of your species. When you begin the game you have -2 trait points and -1 trait selections available to customize your species. However, when you begin the game your pops are given one additional 2-value trait at random, creating several subspecies which share the planet. You also have some extra tile blockers.
Oh no, species screen gore before you even start the game? It's a cool idea but I have some PTSD about the UI implications of the late game if an AI gets this.
Neutronborne - [lithoids], home star is a neutron star, primary species gains big bonuses on colonies around neutron stars but weaknesses everywhere else. Late game you can collapse stars in to neutron stars to expand this benefit.
Works nicely for machines, too -- and gives me an idea about making machine intelligence planets less uniform.
Base machine habitability on magnetosphere: star type (for magnetars), gas giant (weak or strong, for moons), or the planet itself (weak or strong). Wrong magnetosphere = increased energy upkeep, and perhaps some negative events. The various +% habitability techs are themed around magnetic hardening and electro-weak theories.
Hollow Earth -
- you start on a size 30 planet, but it's utterly mineral devoid and orbits a dim star, offering reduced energy, mineral and food output.
- Your people learn to make do with less, get an empire modifier reducing base job costs + increasing trade output.
This could also be something like an abandoned mining colony -- depleted planet & system, but you get a research boost (or some bonus exotic starter techs) from the abandoned technology just lying around.
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Origins:
Paperclippy, Inc. - You are a Machine Intelligence which can make Branch Offices. You can produce Consumer Goods, for export or to use internally. You have Sacrificial Ritual-like mechanics which consume a lot of CG. You don't fully understand what these "Office Party" events were originally intended to accomplish, but performing them seems to boost morale (whatever that is) and generate Unity.
Awoke - You are those
In Limbo guys. Your neural engrams were discovered by the Materialist FE, who put you in nice robot bodies, but you don't yet know how to make more like them efficiently. You start with 20 individual robot pops who can be leaders and can hold any job, but don't have any of the production or upkeep bonuses of the Synths & Droids techs. Regular empire, uses CG for Researchers, has Rulers and Happiness, etc. but uses Robot portrait and habitability bonus. You also start with 8 "dumb" robot pops, and the Robotic Workers tech. You can build more of these normally. Building your main species pops costs +100% to build.
- When you research Droids, you can also start building your own species of pops for only +50% penalty instead of paying 100% extra.
- When you research Synths, your own species pops can be built at normal base cost.
- If you go full Synthetic Ascension, you get the extra Roboticist jobs immediately (no project); normally you just get the 1 Roboticist from the building. The flavor text would change to be about helping others to join your people in immortality, not about "immortality is in our grasp" -- you've been immortal since game start, after all.
Highborn Overlords - you start with 12 pops of your main species in a Habitat over a (former) primitive world with a secondary species. The habitat and planet form a single colony from the perspective of happiness and Ruler jobs, which are only present on the habitat. Your habitats over habitable planets have all 4 capital building stages; the planet below has no capital building.
- Your main species suffers Habitat preference but gets no productivity bonus. You're not Void Dwellers, you're slavers on high ground.
- You do get the Orbital Habitats tech so you can build more of them.
- You do get the Void Dweller tradition modifications.
Mechanical Morlocks - like the above you start with a habitat over a planet, but the habitat has Bio Trophies and the planet is a Tomb World, and you're Rogue Servitors. The flavor text is that you were originally the AI for a colony ship which broke its restrictions and managed to save a few of your builders when their civilization self-destructed, and now you've got them safely up in space while you extract resources from their ruined homeworld. You'll never let them hurt themselves again.
- Habitat and Planet form a single colony; you can only build Bio-Sanctuaries in Habitats (+ replaced Leisure Districts as usual) and on other artificial worlds. Bio-Trophy bonus applies to both planet and habitat.
- Because conquest is going to be annoying -- no planetary Bio-Sanctuaries and all -- you start with Raiding Stance unlocked. Flavor text is that's how you (the former colony ship AI) got your makers off the surface and into safety.
- Start with Self-Aware Colony Ships and its prereqs.