I've been playing GalCiv2 for a couple of years and I've made my list of features; some of them has already been posted, but, you know, repetita iuvant.
1 - Civilization borders. I know that this has already been discussed, but I think that there's a solution to the problem of being sorrounded. Currently we have (at least in Twilight of the Arnor) a UP resolution that (if approved, naturally) charges some taxes to a civilization that has starbases inside the area of influence of another civ; also, evil civs automatically "tax" foreing trade routes passing inside their area of influence after they research the ethical alignment branch.
My proposal is to make this the default behaviour for every race. Instead of being unable to transpass someone else's border, "civil" ships (that is, freighters, constructors, colony ships, miners, scout/survey) are charged with a certain amount of Credits every turn as long as they are in someone else's territory.
Military ships, instead, can't trasnpass at all, or at least are tolerated for a variabe amount of time depending on the relationship between the two civs; when patience is over, the choice is war or to send the ship back to neutral/friendly territory (like when ships are sent to an area outside teir range by a wormhole). This way you can't crowd your fleets around someone's capital planet before declaring war.
Of course civs should be able to negotiate their right to pass through freely, with a treaty for civil ships being easier and cheaper to obtain, and a treaty for military ship being harder and/or more expansive. A military pass should also work as a non aggression treaty and if you attack the civ that granted you free pass, you shold have serious diplomatic problem with all races. An established trade route with that civ can be considered a free pass treaty for that single route that doesn't affect other ships.
2 - United Planets. Well, now the UP isn't that great. It should be more interactive, with the ability to propose topics and a turn of encounters with the other civilizations before the vote to see what they think about the law in discussion and maybe make agreement with allies, or trade with a civ for a friendly vote. This also helps those civs that have too small voting power to influence the decision.
Also, when playing at normal and lower difficulties, it's too easy for the player to gain 50% or more of the votes, wich can make the UP something like a legalized chat. I think that no civs, no matter how big they are, should get enough voting power to be able to vote a resolution without the help of at least another civ.
3 - Shipyard #1. This also has already been discussed. Upgrading a ship shouldn't remove all the funcional parts. Maybe I just want to change the engine with a faster one, or worse, I just want to add some eyecandy to the design, why should I be forced to replace everitying?
4 - Shipyard #2. Idem. I think that there shoud be some way to restore an obsolete ship, just like in TOTA you can build obsolete buildings from a separate list. You never know when an old design can come in handy (because it's cheaper, faster to build or whatever).
5 - Shipyard #3. Not the biggest problems, but there suold be some way to rename the class of a ship without upgrading it. When I build a custom set for a race and I re-use it in next games, I usually call the most modern designs with progressive names (i.e. mark1, mark2, etc.). I know that it's not a big deal, but if I need to add an intermediate model I'd like to rename all the other available ones to keep the right progression.
6 - Trade goods. Now, trade goods can be only traded for money or something else once. Instead there should be, like in Civ4, the possibility to sell them for a weekly revenue. Or, even better, they should affect the value of every trade route of your civilization and not be sold via the diplomatic screen at all.
7 - Constructor Ships. I think that they should behave like miners: it takes a certain amount of time to build the starbase, but the ship isn't lost in the process.
8 - Distance between civilizations. It can be good to add a new parameter for sandbox galaxies that allows the player to choose how far the civs are at the beginning of the game.
9 - Pacifical conquer. Already been proposed. There should be a diplomatic path to conquer small civilizations and even the bigger ones, provided that the conquering civ's power is much bigger.
10 - Internal commerce. This is partially linked to the idea of territory and borders. In Civilization, the cities and resurces are connected only if they are linked by some means of transport (rivers, roads, ports, etc.). I suggest that in GalCiv 3 planets and starbases can share their resurces and benefits only if their influence areaa are connected directly or indirectly (I mean, direct connection between each other or connection to a large "bubble" of influence made bay other planets/bases).
If you have a group of planets or a minig starbase that is separated from your main influence "bubble", you have to either expand your area of influence with new colonies or with starbases or manually link them via internal trade routes; those are not limited like the ones between civilizations. I think that now it's too easy in the mid-game (at least in normal difficulty) to race to resources and best planets and have your empire scattered through the galaxy without any real drawback, except if you ere aiming to an influence victory. The feature I propose should led to a more smooth and planned expansion.
11 - Escort. There should be an option to add some military ship as escort to a civil one. I'm specially tinking about freighters, as other ships can be grouped in fleets. Once a freighter has established it's route, however, it's alone and can be easly raided by enemies.
12. Ok, this is silly. Just eyecandy, but it's a thing that bugs me a little. Starports, if will still be there (why not?), should be renamed dockyard or something like that. I mean, a freighter can land on any planet, not just the ones with starports, and I assume that there is some private/passenger/commercial traffic between planets. So it's safe to assume that every colony already has a starport, meaning some sort of facility where ships can land and take off. What they actually miss is a place where to construct ships.