Some of these ideas are probably already posted:
1. Military starbases are the only structures able to build the biggest size ships after researching and building some modules. Once you research a new hull size you should be able to upgrade your starport to be able to build the new hull size. Starports can be upgraded and are only able to build up to large sizes.
2. New hanger modules (up to three?) to add to military starbases, one hanger gives free maintaince for one ship, the most expensive ship first.
3. Constructors- Max number of constructors depends on your logistics ability. The constructor module is now very expensive. Click "Construct" and select a starbase on the galactic map, then select the module you want to build. The constructor will automatically go next to the selected starbase/etc and start to build the module. Can have multiple constructors assisting each other, but the reduction build time is low. Ex. A module that takes 10 turns to build with one constructor, adding a second constructor to assist will only lower build time to 8 turns.
4. "Abandon Planet" option - The population on the planet will decrease rapidly migrating to the nearest planets. Everything including buildings/etc on the planet will remain intact. Needs some contermeasures, can't think of any now.
5A. Barracks (One per planet) - Trains your own population into soldiers. Regiment of troops or units.
5B. New buildings to train invasion troops (all are "One per planet") - One trains regular soldiers/tropps, 2nd building/factory manufactures mech warrior type invasion units. Another new building manufactures tank type invasion units.
Each race has at least three invasion troop types and they're different for each race. Ex. The Korx can hire powerful mercenaries with a special building. The Thalan empire will be able to build giant spider type units, organic or robotic. Each type of invasion unit takes up different space on transport modules. Your own soldiers takes one space, mechs take two spaces (one mecha = 2.5 soldiers), tanks take three space (one tank = 4 soldiers). The more powerful units takes every long to train/build. Once you build the barrack type buildings your planet will automatically start training/manufacturing. Once you research a certain tech the tech is unlock for ground forces. Ex. After finishing researching lasers, laser rifles is available for your soldiers, same goes for armor and defenses.
6. Pirates- Ships can randomly spawn in a undiscover parsec, near trade routes or planets with low approval rating. Pirate bases can also spawn, pirates can send ships and transports to conquer nearby planets. If the bases are left alone for a certain amount of time, bases will be upgraded. Can establish contact with pirates and tell them to attack your enemies with bribes similiar to Sins.
7. Able to research multiple projects at one. A slider bar similiar to MOO1 where you want to allocate the percent of your your research points to a certain category. Defenses, Weapons, Propulsion etc.
8. Speaking of propulsion, different fuel types? will affect your range along with life support systems.
9A. The star/solar system Stohrm mentioned above was a good concept in MOO3. Less micromanagement on the galactic map. Makes it easier to defend solar systems also. All your ships in the solar system are pooled together in the same system.
9B. MOO3 had system ships etc, ships that can't leave the solar system, they were much cheaper for maintaince.
10. New tech to build space/star lanes, warp gates, star gates on each solar system. Lanes and gates reduce movement between each solar system.
11. "One per system" buildings - Many new buildings, in addition to the above lanes and gates being "One per system" Build one and the bonus benefit all planets in the solar system. If your opponent already builds one before the player, the player can't build any in the same system.
12A. Weapons mounts - Point defense, Normal, Heavy, Very heavy, Ultra mounts
12B. Weapon modifications - Shield piercing, armor piercing, etc (Depends on what weapons, some beams get SP, some mass drivers AP)
12C. Armor mods - Very light, light, normal, Heavy, very heavy, Ultra heavy
13. New weapons - Each weapon is split into at least three types. Beam, Missles, Mass drivers
I. Surging/focus weapons- When you fire the surging weapon at the enemy ship the beams will stay focus on the ship till it dies or player changes target/moves ship away. Naturally shield and armor piercing. Surging weapons are very effective at taking out large ships with high HP. Once you kill a target it takes a long time before you can select your next target and fire it gain. Ex. After one second your ship might do 10 damage per second, two seconds 30 DPS, three seconds 60 DPS, four seconds 100 DPS, five seconds 150 DPS, etc. One counter for this, is to move out of range.
II. Beam- Regular beam weapons, normal damage and range.
III. Devastator/bending? Beam - AOE beam type weaponry. Ex. After you fire the beam on the left, the beam is capable of moving to the right side if there's a ship.
B. Missle - Energy missle, regular missle, scatter pack (new missle modifications includes small and large, small being harder to shoot down)
I. Energy missles - Anti matter torpedoes, Photon torpedoes etc. Highest damage damage and fast speed.
II. Regular missles - High damage and the fastest speed
III. Scatter pack - One big missle launch can split into 2-3, then the 2-3 can split into 2-3 again when they get near the enemy. Since these missles are smaller size, they're harder to shoot down before it reaches your fleet. Medium damage and medium speed. Ex. one large missle can split a few times into 10-15 smaller missles, or if the large missle is shot down, it splits up into smaller missles.
C. Mass drivers get maybe an "explosive round" mod to deal damage to nearby ships.
14. Heroes - Can recruit heroes from different races, depends on your influence. Not sure if you want to seperate them into admirals (battle only) and governors (planets only). Each hero has at least three planetary/fleet skills, two system/whole fleet, and at least one super skill. Planetary/fleet skills only benefit the fleet and planet hero is on. System/whole fleet benefits every planet in the solar system/fleet in the battle. Super skill benefits your whole empire.
15. New Techs
A. Anti-beam field - Can only be use once per fleet per battle. Beam weapon effectiveness reduce near area where is it deployed. Can work both ways, ex. it can also reduce your own beam weapon effectiveness
B. Stasis field - Disables ship engines/fleet unable to move for one turn. They can still attack.
C. New special weapon that pulls the enemy near your fleet when used. High cooldown.
D. New special weapon that pushes the enemy back when used. High cooldown.
16. Percent population on planets - Ex. 50% Human, 25% Thalin, 25% Yor on one planet. Good alignment races get bonuses, Neutral ?, evil races get penalties. New option if a planet is multi race, "Destroy <race>" evil alignments will get a bonus after that, ex. morale. Your race's migration to other planets depend on their loyalty.
17. Organic ships - Maybe from a new race? Their ships can swallow other ships and heal, the organic ships can split acid in place of other races' beam weapons and has strong short range melee attacks. Acid has a poison effect. They can also launch mini organic alien ships. They almost act as carriers.
18. AI demonish buildings - New AI lines added to remove useless buildings later on in late mid game to end game. Say add the following line to "Recruitment Center" and other population/temp in PlanetImprovements.xml for each race "<Demonish> yes/no" then follow by variables when it will demonish the building. "<Demonish> yes, Variable one = 75% population, Replace with <specialize>". Makes the AI smarter, I saw the Torians (Ultimate AI) with max pop on planets still with "Recruitment Centers" and a few "Fertility Centers" all on multiple planets. AI will now demonish the recruitment center when the planet has 75% or more pop, and replace it with any building that the planet is specializing in. Maybe each race can have different lines for the same buildings. Say for the Torians you want them to Demonish or stop building the population/temp buildings when a planet reaches 75%, but for another race 90% population. A exception line to a certain faction AI to stop building a specific building or wonder on a certain planet such as the Thalan's building Hyperion Matrix right from the start on their cap with 300% food tile! their cap can now support 48 bil.
19. Spies/Espionage- Spies can now framed other races for sabotage, stealing techs etc. If you place spies on tiles they can sabotage buildings, high cost to repair the building.
20. Food - Different races consume different amounts of food each turn. Races such as the Yor do not comsume food. Farms now feed people throughout your empire, not increase the max population on a planet. Extra food is sold automatically for extra money. One special tech to grow a small amount of food on planets which food can't be grown, such as a toxic planet.
21. Every planet has new ratings (gravity, resources, farming, research, influence) the ratings were previously in tiles from GCII, they are now planet wide, but the bonus is greatly reduce. Planets now all have a gravity rating very low, low, normal, heavy, very heavy, extreme. Many new techs to reduce gravity effects. Resources (manufacture rating) - very poor, poor, abundant, rich, very rich, ultra rich. Farming, on non Earth like planets is usually poor or very poor unless you have special techs available.
22. A new solar system near the center of the galaxy with all high PQ planets, Ex. one planet is ultra rich, one has artifacts for a big research bonus, one main planet has all of the bonuses. This solar system was abandoned by an ancient race for some reason. Maybe this could be link to some event, the ancient race will send scouts/small ships back to their solar system by a portal near the new solar system. The ancient race will continue to send scouts thru portals in nearby systems harassing other races. Every race in the galaxy declare areas around this solar system "Neutral Space". Anyone can freely attack anyone without any diplomatic penalties. As time passes by the ancient race will send more and better ships through the portals. Your race can now research these portals. After multiple research you can build/use a portal of your very own and send your ships to take the ancient race's solar system/galaxy. Maybe in an expansion, the ancient race is in another galaxy fighting a winning war with other races. The solar system you took is just one solar system of many.
23. Team play - Better team play options, able to select teams when starting a new game. Ex. Three or four teams with 3-4 races each on each team. Say I have two other races on my team I can tell them what techs to research and what planets to invade/attack, etc. Your team's influence/etc is combine if going for an influence victory, etc. If "Tech trading" is check, races on your team will automatically get the techs you just finishes researching and vice versa, except maybe for some special race specific techs. Team play in Civ4 was good.
24. Able to restore a planet/tiles after the planet HQ drops. This takes a long time and players cannot purchase.
25. Five new Housing/Population increasing techs - 1. Tech that lets players build subterranean/tunnels bases underground, increase the planet max population. 2. Tech allowing players to build bases on moons if the planet has one, increases pop cap by a small depending on sizes and number of moons the planet has. 3. Techs that allows huge space stations orbiting the planet to be built. In battle these stations can be destroy and people die, with diplomatic penalties. 4. For only aquatic races such as the Torian, they have techs to build underwater domes/cities. 5. Planetary Reorganization: A new housing plan to better reorganize the planet so it can fit more people.
26. Initial Colony and starport no longer take up tiles on planets. They are infrastructure improvements such as the housing/population techs above.
27. Able to select different galaxy types similiar to different type of worlds in Civ 4. One type of galaxy is flat, the one we have in Gal Civ 2. Second type of galaxy is long, means if you have any ships that are near the left edge of the galaxy they come out in the right side of the galaxy and vice versa. Tall galaxy it's the top and bottom that happens. Round galaxy it happens at any edge of the galaxy. In total four galaxy types flat, long, tall, round.
28. 64 bit only? by time GC 3 comes out I think it'll be 2014-2016, by that time 75-90% of people will be using 64 bit systems. The only ones with 32 bit windows might be really old business computers.
29. GC 3 created with DirectX 11. Time to ditch the 15 year old Windows XP and and 9 year old Windows Vista. By that time I think we'll have Windows 8 and Windows 9 along with the currect Windows 7.
30. New feature to create your own leader with their own abilities.