Something i would like to see is war made into something closer to a political game. i mean the point of a war should not always be to cause the genocide of your enemy. It would be interesting to see war between civilizations as something of a negotiative means. it works a little bit like that now if you put starbases near someone's planets, and they might elect to go to war with you to destroy those bases because you won't move or demolish them. the problem is, the AI generally that ive seen does not offer for peace unless they are losing, won't accept a peace offer unless they are losing (or if youre losing you pay them a LOT to back off, which you tend to not have because you are losing). now, i am not saying i dislike war how it is, but i think it could be so much more. your people are going to have an opinion of the war, and how things are going. this should affect more than just trade with the one enemy civilization. you wipe out someone, and the other races are gonna fear you. you do it too much, and they become hostile toward you. while at war, your people don't have to hate eachother, and in fact, there could be a use for propaganda centers now to make your people feel more distrust of a civ you are at war with. it would be easy to simply put a value on citizen's trust of each other race, and boost military production (or cut it)to match. i mean, if i have friends in a country that the US is at war with, i certainly am not gonna try so hard to help produce weapons that might ultimately my friends. on the other hand, if i beleive (or am led to beleive) that a certain country is evil, and filled with people who don't deserve to live, i will be much happier making things that might destroy them. this is exagerated of course, but it doesn't have to be in the game. in fact, the ability to make someone trust you more and/or the ability to sway your citizen's trust faster could become abilities added into the game.
just my 2 cents of course.
other things:
i disagree with the ability to destroy a planet. this game is not part of the MOO series, and i think that planet destruction brings it closer to being so. more importantly, the planet, if it has people on it, could be useful to your people, don't you think? makes more sense to invade it, and kill or enslave the native population, while strnegthening your own empire. planet destruction would certainly intimidate your enemies, yes, but unless you are playing a bully, how many enemies are you really gonna have.
expanded espionage would be kinda cool. the already suggested idea for espionage victory would probably be cool if its done right. I would kinda like to see technologies that incerease your espionage abilities. like you develop a small invisibility cloak, now your spies can hide easier. gain +15 espionage. something like that. It would seriously require a lot of money put into espionage to win like this. The AI would need to be able to put money into espionage. I have to wonder what fun could be had on an unsuspecting player if you have deep espionage roots in them and can manipuate them without them knowing.
more invasion options? what in blazes for? choice one: invade or don't invade. choice two, do you plan to utilize the planet, or simply wipe the species there off of it? there are already choices for this depending on your intentions which determines how many planet improvements you destroy, ect. ect. while it would actually be interesting to see your ground units equipped with, say, personal size weapons in any one of the three categories, and have the oposition attempt to use defenses accordingly, that almost feels like that is what the advantage factor is for. you also don't want invasion to become a second ship combat phase. In my unabbreviated opinion, more options for this would prolong it, and make it more of a chore than it already is.