Here is a list of suggestions that I have made over the years, some of which could be by applied to GC2, and some of which would probably need to wait until GC3:
1. My personal #1 is still the constructor grind. For the love of god, please allow starbases to self-upgrade. Upgrading them should be a simple matter of queuing up modules, much like queuing up planetary improvements. You could, perhaps, leave in the ability to use a constructor to perform an instant upgrade, rather than waiting on the starbase to complete its own upgrade. For key installations, this would be a convenient and vital thing. For the vast, VAST majority of starbases, however, setting an upgrade queue and leaving them to their own devices would be much more convenient.
Or how about a governor that can keep track of every starbase, letting you set how far you wish to upgrade it, then automatically routing all constructors to multiple starbases at once? I should be able to plan out in advance what upgrades a starbase will get so that I don't have to decide on an upgrade for multiple bases many times each turn. When you have 30 to 40 starbases, all in varying states of construction, and just about as many planets building constructors, it can get a little hard to manage.
If you don't want to make starbases self-upgradeable (but I really think that you should), would you at least consider making starbases automatically a rally point as soon as they are created? I build lots of starbases, and having to build create and name the corresponding rally points for the constructors to find gets to be a pain, especially since the rally point into window still has that strange bug where, when you click on the rally point name, the cursor goes to the beginning and you have to move it all the way to the right and delete the generic name before you add your own.
2. Make the United Planets useful and meaningful. Right now it is virtually useless. Give the player some real influence over the council. Using Sid Meier's Alpha Centauri as a model, allow us to buy/influence votes, introduce bills, broker deals, anything.
3. Give the government choices some meaning as well. I hate to make the obvious comparison, but SMAC and Civ IV do this right. You don't need to copy them, but make the choices something more than just a good/better/best/bestest progression. There should be good reasons to stay with one type over another, or to switch back to an older form. The current system is far too simplistic.
4. This is something that never made much sense to me. If the humans developed the FTL drive, and the other races aquired it from them, why is it that all of the other races start off as 'unknown' to the terrans. I mean, they always start out first contact by thanking the humans for the FTL drive, but that seems to imply that they've already had contact. What's up with this?
The way I figure, the Terrans should always start a game with at least one other race already discovered; the Altarians would be a good choice, especially if you see them as a kind of offshoot of the Terrans. Then you can simply hypothesize that the other races got it from the Altarians, without the Terrans needing to have discovered all of them.
Or, even better, let the Terrans be the only ones with FTL tech at the start of the game, and give all of the others the stargate tech. That could be interesting. Let the Terrans actually play out the passing of FTL tech to the rest of the galaxy.
5. Change the population/garrison system so that population is calculated separately from soldiers. It doesn't make any sense that my troop transports can hold about 4 BILLION people per module. This just isn't physically possible, and it doesn't make sense for me to have to so deplete the population of my planets to stage an invasion.
6. I would also like to see some diversity in spy missions. Perhaps let us destroy improvements altogether. Or make it so that the type of improvement a spy is placed on dictates the type of mission: place him on a research improvement and he focuses on stealing tech, on an econ improvement and he steals money, on an industrial site and production for that planet is hampered. Maybe something really interesting could be devised for placing the spy directly on the initial colony site; planetary subversion, perhaps? Who knows? Hopefully these suggestions are actually possible within the current GalCiv2 engine. But I certainly think that they should be addressed by the time we see GalCiv3.
Those are my top six. Enjoy.