All good points and I do agree that the early game land grab needs to be kept in check but I'll have to show my biases here and say that I'm not a fan of the population management aspects of most 4x games. I also really dislike having to go back and upgrade individual ships after researching a new technology. Philosophically the choices in Empire are more about what you want to research as opposed to research vs. production vs. population.

The population growth changes that will be going in the next server update will help with the problem somewhat and will make investment in technologies like terraforming, planetology, and genetic manipulation more worthwhile. I also think a shipyard equivalent for planetary control could work quite well in addition to some cost tweaking on the outpost / colony ships themselves.