Native Races

There are neutrals already in the game, though not like they are in Moo3
Since planet values are the same for all players (Good conditions are good conditions for everyone), creating really distinct races is rather difficult.

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That is an interesting concept in some ways.
Perhaps there could be a few types of said races.
The most basic ones, having little 100kt size 'villages' that each has a meager mineral and organics output and effect their population (making them 'separate' from anyone who colonizes) and count as a race that breathes the default atmosphere.

Others could be an industrial age one, a well populated planet with good industry and resource production, maybe limited research and espionage output also. They could have a few lvl 1 troops and fighters (fighters not space capable), and maybe a satellite in orbit (no weapons, just lvl 1 basic sensor and sat core, sort of like a space telescope of sorts)

Another thing would be an early space age race, they can build space stations, fighters, and satellites, but have no weapon platforms, and maybe be stuck to have a few 'special' ships that are more or less slow and lumbering compared to regular ships (such as 1/2 normal move, -50% defense, half normal turn speed, etc).

Maybe they could have their own little traits, and offer their own bonuses, like perhaps a subterranean race that gives the planet a bonus to mineral production, or a race that is great with plants giving a boost to organics production, etc.

There could be penalties for moving them to another planet, or wose, or 'spacing' them (unless race is Bloodthirst, or maybe has the Xenopobic thing).

Other options could be special tech that they unlock in a manner similar to ruins, allowing to research it to get a new component, facility, being able to build more of their buildings (or spcial buildings) on their planets, or maybe something that allows for small empire wide bonses.

The only obstacle is how to even get such stuff into the game...