There will be terraforming. You will be able to change planet type one or two times. Desert-Terran; Volcaninc-Desert-Terran; Barren-Volcanic-Desert, etc.
These are just examples, we will decide what types of planets you will be able to terraform to some other type, and it will depend on your tech level.

About colonies, they just take some time to develop to the level of the Homeworld but canonically speaking in Star Trek there were important big colonies like Deneva colony, Alpha Centauri..... Plus the empires that are not very open to aliens like the Klingons and the Romulans would have a more difficult time expanding.

There are examples in Earth's history where the colonies grow to be larger than the founding nation. I would not like to limit the colony to a lesser potential. I would like it if taking the "home" world did not mean the end of a race in the game. There are games like Age of Empires where you can set up a new home base. Unfortunately the capture of the one home world rule has long been coded into the game and it can't be change for Supremacy.

Wait, if you lose your Homeworld, you lose the empire?