I think there should be a good balance between vertical and horizontal growth.
Astro Empires example
With the issue about spamming colonies, Astro Empires ( http://www.astroempires.com
) has a simple yet effective means of limiting colony expansion.
You build colony ships for 100 credits. When a colony sets up the first base, you have to pay 50 credits (upon landing colony/setup base). Next base is double last, so 100 for 2nd base. 200 for 3rd base, etc.
This game is real time, so building your first research lab might take 10mins and cost 1 credit, 2nd level research lab will cost 5 credits and take 20mins, etc. So the idea is to spread fast early on, cause you can get a bigger economy by leveling up your buildings on multiple bases, then doing it on one base. But by about the 5th base it is harder to make a sixth base when it costs 800, so you need to do some vertical growth in between.
Population growth rate
Along with the idea of colony ships taking population and putting them on another planet, population could grow faster if there is more population on that planet.
Eg a 5000 pop world gets 1000 this turn
a 2000 pop world gets 200 this turn