Suggestions for GalCiv II
The things that I myself would like to see most are:
1) A much more in depth management of the individual planets. Maybe being forced to deal with polution on an individual planet, much more of the ethical choices (although they should be less obvious than good, evil, and neutral (this is by no means a criticism on the current system, I like it very much)). Planet invasions could consist of some kind of mini stratagy game taking place on the planet (similar to the total war series, where the battle map is real time and you control the unit squads).
These features should also be able to be handled by the AI (for the more casual gamer).
2) A life-like economics system with actual supply and demand, demand pull and cost push inflation. Recessions. The amount of exports and imports depending on the value of your civ's currency. There should also be options to set fiscal and monetary policy (fiscal being changing taxes and gov't spending, and monetary policy is the actions of the Fed.) On importing and exporting, I think the player should be able to make actual goods that they can trade with the trade ships (but also consume). That way you get specializations in trade advantageous to both parties, making war more economically damaging than it already is.
Sorry for the long story, but I hope it will serve as an intro to a long list of replies.