Scrolling in ship design
Badly need to be able to scroll as well as rotate (Yeah there are fancy names for such camera movements, but I'm too lazy to go look them up.) as it becomes a nightmare trying to design anything funky once you start making big ships
Better hookpoint rotation
I've been driven to the edge of sanity trying to rotate hookpoints correctly, not only that but if you rotate a hookpoint multiple times, trying to figure out how the hell you get it to turn through 270 degrees without going nuts on you, the hookpoint modifiers stack up to gargantuan numbers making it annoyingly slow undoing your changes.
So to cut a long run-on sentance short, hookpoint rotation needs to become much less painful.
More UP interactions and stuff
Highly descriptive I know. Would be nice to be able to propose new UP resolutions, call an emergency UP session (Drengin are wailing on the poor defenseless minor races so need a UP smackdown, for example), know the proposal a week in advance giving you time to trade for influence to tip the vote, espionage to know in advance how someone will vote, all kinds of things like this. I have fond memories of manipulating the Orion Senate in MOO3 with my underhand dealings and sneaky actions.
For the love of cheese sandwiches, fleet management needs a serious overhaul
After designing my ships, going not-quite insane putting the hookpoints the right way around, my sanity was liberally shattered when actually attempting to do anything but move my fleets around. Anything you can do with a single ship, you should be able to do with a fleet. The UI is meant to be a way of communicating your wishes to your pooter. It's not meant to be an exercise in trying to outwit it and come up with clever inventive ways to bury its liberal ideas of 'functionality'. Please, think of the children, fix fleet management.
More diplomacy options
Diplomacy is already nice and robust, and funky, but it could be made more funky than a glitterball on steroids with some simple additions. The option to send a generic 'threat' to an AI would be handy, the option to demand/negotiate a regular tribute payment (i.e an amount of bc per week, every week, for a determined time), a generic 'get the hell out of my bloody space' for those ships that sit in your space but don't seem to do anything but clutter up your nice clean spacelanes, things like this.
More things to do with a fleet and an enemy planet
Would be nice to be able to 'glass' the planet using my death-dealing ships. I again have fond memories of parking fleets in orbit around a Harvester world and blowing the parasites to hell (and back), and then doing the same with those backstabbing dastardly Nommo. Since planets are nominally self-sufficient, there's no point in blockading them, but blowing them away would be nicely satisfying.
Espionage
Being told when two AIs end war is nice. Being told when two AIs go into war would be even nicer. Espionage could also tell you who is trading which techs with whom. Would be yummy to be able to select different kinds of espionage, be it social destabilisation which reduces influence, miliary espionage which could tell you what is being built where, when, economic espionage to tell you which trade routes are their most profitable, and so forth.
Unique Technologies
A way to flag a tech as unique to a particular race (i.e. only one specific race can research it) would be good, same with flagging a tech as 'non-tradeable' (I fail to see how you can trade something like increased diplomacy to someone, it's a bit esoteric), also techs that work like trade goods in that say Drengin develop uhhh, Matter Ownage Cannons (Creativity is not my strongpoint, but feel free to use that name. It has a ring to it...), and only they can fit them to their ships. But they can trade them to other civilisations.
Which leads nicely onto...
Trade Goods
I'm semi-disappointed with the way these work in the game. I was expecting more detail to them rather than a one-time trade to an AI. It would be good to be able to negotiate the trade of say Micro Repair Bots for 26 weeks, or Ultra Spices for an indefinate period. The person owning the trade good can cancel the 'contract' at any time, but then suffers a big relations hit, the person getting the goods can cancel but loses nothing essentially, 'cept the goods.
Hrm, that's all for the moment. No doubt I'll come up with more later, but that will suffice for the near future.