Some feature requests for modding.
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Improvements should also be able to give "flat" bonus (raw production) in addition to the percentage bonus (Manufacturing, Research, Wealth, Approval, etc.).
Ex:
Factory X: +10 Manufacturing points, +10% Planet Manufacturing.
The same for:
Planet Bonus (ex: Wobble, +10 Wealth points and +50% Wealth, +10 Research points and +25% Planet Research).
Planet bonus from "colonization events" (ex: +20 Research points and +50% Planet Research).
Tile Bonus (ex: Mountainous, +5 Wealth points and +25% Wealth).
And also for:
Race Traits Bonus, Starbase Bonus, Tech Bonus, Events Bonus, etc.
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The goal is to remove the adjacency bonus system, to replace it by a system based on the number of same type of buildings built.
I think it's already possible to remove the adjacent bonuses for the improvements and the planet tiles with the xml files. If this is not the case, ensure that this is possible.
Ex:
For 1 Factory built, it gives +10 Manufacturing points and +10% Planet Manufacturing.
For 3 Factories built, it gives +30 Manufacturing points and +30% Planet Manufacturing.
So there is no need (and no gain) to build the improvements with adjacency, and the bonus tiles only give bonus on the primary tile.
Adjacency system can be fun with less than 10 planets, but it becomes time consuming, boring, and micromanagement hell with more planets.
Also, it "forces" to build a certain type of improvement on a tile (why not), and it "forces" to build a certain type of improvement on the adjacent tiles (it's too much), else all the bonuses are wasted.
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Add the possibility to have conditions to be able to build improvements depending the planet type and the race.
Ex:
This Automatic Factory can only be build on Radioactive World.
This Factory can only be build by Altarian race.
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Add the possibility (with the xml files) to auto upgrade instantly all Starbases with the unlocked modules, when a technology that gives modules is researched, instead of having to build lots of constructors to upgrade them.
Manage hundreds of constructors is not what I call "have fun", dying should be more fun. 
This increases the game time unnecessarily with "mechanical tasks" instead of "reflexion tasks" more revelant for a strategy game.
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Add several settings, somewhere in a xml file, to remove the "only 1 per turn" penalties, for the research of Technologies, the building of Improvements, the building of Ships.
Why generate lot of Manufacturing/Research points, and be restricted to "only 1 per turn".
Ex:
When your sponsored Shipyard by 2 (or more) planets, can potentially build more than 1 ship per turn, it's better to build another Shipyard with all the consequences that entails, a spiral of micromanagement, time consuming, boring, not fun, "mechanical tasks".