I finally grabbed a copy of Galactic Civilizations II, and I must say I am kicking myself for not buying it sooner. At it's most basic level it is a Civ 4 clone, but in space! Research, economy, tech trees, exploration, etc. It's all there, but the cool part is that you get to custom design your own units if you want. Periodically you get canned Ship types and components to play with, so if you don't like A-scoutship_01, you can design it exactly how you would build it. Your colony ships are your "settlers", etc., so if you want an absurdly fast colony ship for some reason, you just go and build it. It's definitly worth checking out if you have not already.