FreeOrion

Simplest is the elimination of 'population' except as a fluff number.

Replace it with Development/Infrastructure.
That can be "built" into the colony ship in the normal sense.

I also don't think it's worth the player's time to worry about where his population is coming from.

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We already have "Infrastructure". While it's not inconceivable that population could be rolled up with infrastructure, we'd loose some interesting possibilities if these two concepts weren't distinct.

* Smart Weapons that kill civilians without destroying infrastructure. A cool late-game weapon. It would be a huge advantage to be able to conquer a planet without needed to rebuild the infrastructure.

* Humane weapons that destroy infrastructure and buildings while leaving citizens alive. (this is less compelling than "smart weapons."

* Abandoned colonies: I.e. you have development, but no people-- a boost for starting your colony

* Slow Evacuations/Repatriations: Ideally you should be able to remove the citizenry of a planets to allow a new species to settle without loosing the development of a planet.

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All those can be modeled by a distinction between Infrastructure and Resource meters.
Infrastructure=generic slow improving economic capability
Resource Meters=resource specific more rapidly improving economic capability

There is no need for population unless there is migration
If there is migration, then there is no need to worry about where a colony ship gets its population.