Story ideas that I'll probably never do anything with.

Untitled: Supreme Commander/Warhammer 40,000
Supcom/Warhammer 40K crossover quest, inspired by the Supcom/Muv-Luv Alternative quest on Spacebattles. Basically a UEF Commander and his ACU, following the events of FA, are stranded in 40K because Quantum Bullshit, stuck in a human star system as the Imperium breaks down. In a world where the brutality of the Infinite War would be considered only marginally exceptional, this wayward warrior and his endless armies shall continue to do what he's dedicated his life to doing - protect humanity from all threats, both extra-terrestrial and extra-dimensional. Would include diplomacy, combat and research/tech-sharing.

General game balance stuff
The construction of Armoured Command Units is limited by the ability to synthesize superelements, certain types of exotic matter that can't be protocrafted. Super units like Emperor Titans, Ordinatus units and Necron Doomsday Monoliths also require superelement investment.

ACUs are limited by a unit cap and maximum operational area due to how quantum cores work. It is the production of quantum cores that requires the superelements which cap ACU production.

Research
Integrating Imperial tech into UEF forces, vice versa, or reverse-engineering Xenotech (last one only available if you have diplomacy points with the more radical AdMech elements) usually requires an "analysis" research project to achieve understanding of the tech and possibly some benefits, followed by an "integration" project which gets you the actual benefits of tech-sharing. For example, if you had a captured Necron Gauss Flayer and some radical techpriest friends willing to mess with it, you'd have to do "Gauss Flayer analysis I" to discover how the thing works and develop basic countermeasures, followed by "Gauss Flayer Analysis II" to develop better countermeasures and "Gauss Flayer Integration" to begin equipping your own forces with Gauss weapons.

Research projects have a difficulty rating which determines the chance of success, you roll dice for this. If you fail you can do the project again, if you succeed it's crossed off and you get the next project on that branch of the tech tree unlocked. More advanced tech requires more difficult projects but as you get more of a handle on a tech base you get bonuses - so the Eldar and Necron tech trees start of with everything at very high difficulties, but completing projects on those trees make future projects somewhat easier as the researchers already understand some of the tech and can work from existing knowledge. Certain techs have more than one prerequisite so require multiple research projects to be completed before they can be researched; other techs can be unlocked without certain projects but benefit from them anyway.

Living planet quest (original)
A sapient planet kitted out for war and its population/garrison of humans are cast into a new universe and grievously hurt in the process. Now they must rediscover their technology and learn to harness their magics once again, and explore this brave new world. Involves combat, diplomacy, SCIENCETM and a mixture of optimism and grimdark.