What I would like to see added to GC3 from a modding perspective:

1. The ability to set more than one PreReq. For Example, A Tech and an Improvement, or a Tech and a Ship Component.
2. Redefine how PreReq's work. For example: Player A builds Wonder A which unlocks starbase module A and Wonder B. Player A then builds Wonder B which unlocks Ship Component A and Starbase Modules B ect.
3. The ability to make Improvements or Components Obsolete via Tech.
4. Be able to define a Planet list for factions. Similar to the System list but for planets and each faction.
5. TOOLTIPS :- Defined Tooltips for bonuses that are either colony or faction wide. At the moment if you have an improvement that adds a bonus to both Faction & Colony it displays the same just doubled up: +10% Manufacturing(Local) and 10% Manufacturing(global). If you add a modifier to a Planet Trait that effects say an asteroids mining yield(I added a 50% modifier) it will display as if it is a Planet buff(+50% Raw Production) it does not say it effects Asteroids even though they are set as the target. Put (ship) or (starbase) in tooltips so players know what is effected, as well as tags like (fleet) or (enemy fleet).
6. Be able to add Stats/Modifiers/Actions to ship roles, positive or negative.
7. Be able to add our own Personalities.
8. The ability to add our own Difficulty levels.
9. Be able to add our own Hull sizes.
10. Be able to define how aggressive the Pirate faction will be and how agressive the AI will be towards Pirates.
11. Let us create abilities that do more than throw stats around, like Ancient. Even if a boolean toogle is the only thing, we can do a lot with that.
12. Make <target> able to target individual items(components/improvements/etc) more specifically than it does. Manufacturing can be added to colonies, but I want to add more manufacting to improvements, more damage to lasers, etc.
13. Ability to include more than one of ship/shipyard/starbase as a target.
14. Make it possible to deploy the following events by starbases/planets(/ships?) in their respective sphere of influence:
          <xs:enumeration value="ConvertDeadPlanet"/>
          <xs:enumeration value="ConvertDeadPlanetToThulium"/>
          <xs:enumeration value="ConvertAsteroidsToDurantium"/>
          <xs:enumeration value="ConvertGasGiantToPromethion"/>
          <xs:enumeration value="ConvertDeadPlanetProportional"/>
          <xs:enumeration value="ConvertDeadPlanetToThuliumProportional"/>
          <xs:enumeration value="ConvertAsteroidsToDurantiumProportional"/>
          <xs:enumeration value="ConvertGasGiantToPromethionProportional"/>
          <xs:enumeration value="TerraformTilesOnPlayerPlanets"/>
          <xs:enumeration value="TerraformTilesOnPlanet"/>
15. Add weights to Improvements, Modules and Components. (Seems there is a weight for improvements already, just unused)
16. Make it easier to use custom height maps.
17. Option to have a Faction AI only.
18. Option to have an Ability or Personality AI only.
19. Allow <EffectModifier> to be effected by Scope types. ATM anything other than default results in no bonus been applied.
20. Add Hull types to the PreReq List.
21. Add Components to the PreReq List.
22. Give TechDefs.xsd the ability to have Triggers.
23. Give TechAgeDefs.xsd the ability to have Triggers.
24. Add a Treaty and Relations to the PreReq and Preculsion tables.
25. Add Map size to to AIStrategyDefs.xml.
26. Be able to set a maximum number of x Improvement or Component (Like Civilizations National Wonders). ATM all we can do is set, 1 or many.

These are bug fixes more than a wishlist:

1. Limit the AI to only build resource improvements/components to the number of resources it currently has. ATM they break this rule.
2. Limit the AI to only build one of its Faction unique Improvements.
3. Fix the fact that custom ships do not display Weapon FX other than a red Kinetic Blast.
4. The game not crashing when a tech has more than 8(or was it 7?) icons on it.

Points one and two: In the base game these are not listed in the Governors.xml as buildable by the AI. As a modder I and maybe others have too, added these to the Governors.xml, this in its self seems to make the AI be able to build more than one of each on a single planet, or even faction wide.

Updated with other players suggestions. 25/8/16

I will update this when I think of more