The one improvement that I'd most Like to see (for now anyway) would be a revamp of the building queue, I would like it to have a list of categories, say; industry, research, economy, influence, agriculture, and special. In each catergory you would have all the buildings of that type so that you could choose a lesser form for construction. I know that when I get a planet late in the game I often have to choose from investing a stagering 5,000 bc to buy the first factory complex, or wait 100 turns, both of which simply mean that the planet isn't worth the effort in anything smaller than a huge map.
