The Main things I would like to see are:
- Optional Tactical Space Combat - not necessarily a turn based system (a'la MOO2), could be a system of specifying tactics/formations prior to fight.
- Special Ships - like the aforementioned carriers, or repair ships/stations, and similar ideas.
- Optional Tactical Ground Combat - make use of your civs advances in a more dynamic fashion. Again not necessarily a turn based system - could be more along the lines of priority targets or more involved tactics. Possibly expanding a planetary invasion to take more than a single week (turn), so you can vary tactics per turn and ship in reinforcements, etc.
- Orbital Defence (in-system fighter or laser satalites) systems as a planetary build option (no space - a colonisation center improvement). I don't like having to design engineless ships to act as local defences - if they are tied to a planet, they should be a planetary option.
- Anomalies were a great idea, but they should be expanded on
- wormholes could be permanent: provided enhanced trade routes (bonus for using wormhole) and a research bonus for drive techs - though it must be guarded to maintain control of it.
- The anomalies are not all present when the game starts, but appear as a result of certain random events - meaning that these events should be investigated when detected.
- Greater Racial Variation - races favour different planet types and treat them as different classes.
- Expanded espionage - as in previous posts - specific targets, sabotage, propoganda, espionage enhancing techs.
- Expanded Diplomacy - as in previous posts - tithing, trade discounts.
- I like the idea of special characters as fleet commanders, system governers or ambassadors - though don't feel it is necessary.
- Wider variety of hulls plus the ability to mod/include other designs without replacing existing hulls (if this is already possible can someone tell me how

)
- I like the idea of special sidequests and random events appearing - ie: your ally is suffering from a deadly plague, will you help research the cure?, or: rumours of a ancient artifact have been heard all over - will you follow the trail to find it?
- not bothered about multiplayer - the AI may need some tweaking, but it is pretty good.
- I would like an improved SP campaign