Here is a few things
Some features to add
1. Drag and drop in city query
2. additional visible title after border line
3. additional visible title from hills (if near plains) and +2 to mountains (if near plains, and only +1 if near mountains)
4. additional visible title on the ground near water titles
5. maybe power bonuses/penalties against local life forms depending on difficulty level ?
6. Ability to change keyboard layout
7. double healing on own/allies territory ? and x4-x5 healing in the city
8. adding ability to Trooper fortify themselves +%5 for each turn till +%25 or so on?
9. Government/Laws (Alpha Centauri style) ?
10. May be religion? (like in dead space or BattleStar gallactica Series)
11. Add to seeker ATV and Tanks additional moving point
12. add Hover units
13. Change visualization of differences armors
14. add additional type of borders (to create a country)
15. City government (for the automation of production of anything in specific areas)
16. Add penalty that depend on amount of cities and size of the map
17. Add game speed that affect on production/research/grown/... and depend of the size of the map (example current game speed is good for medium sized maps)
18. Add some kind of menu to create a personal fraction (?)
19. Add water formers and water resourses
20. add ability to build cities on water titles
21. add submarines (with yellow one

22. Add satellites
23. Add espionage
to improve
1. clarity of textures
2. Huge map is not so huge

3. terraforming ! I want to build any kind of title (like in Alpha Centauri)
to FIX
1. to prohibit build a new city within 2 (?) squares from either foreign border (very annoying when your ally settle a new city in your border

2.
P.S. i spend a lot of time on Civilization 2,3,4,5, Alpha Centauri, Call to Power 2, Master of Orion 2.
P.S.S. sorry for my English =)
P.S.S.S. i will add here some of my things...