My biggest wish for the Gal Civ franchise? A robust ground combat engine!
*Ground combat classes (Marines, Infantry, Armor, Artillery, Air Support, etc). Each unit having different abilities, and movement levels
*Planets conquered hex by hex (both by military and influence)
*Partisan units spawned based on resistance level
*Having to maintain space superiority to either do orbital bombardments (or send reinforcements)
*Ship modules providing combat bonuses
Imagine how different the game would be if an invading race were bogged down, throwing resources at a strategically valuable planet for 30 turns?
What if they couldn't conquer the whole planet, but they have an iron-clad grip over the elerium mines that the defending race needs?
Military Academies could have their own queue, with ground units then created on the host world. Instead of just being spawned like a resource and locked in place, they could be mobilized and stationed at strategic worlds.
The planetary map is already built for hex-based combat. Generals could be used to increase effectiveness, spec ops missions for sabotage. It opens so many possibilities to make for an even more in-depth experience in each game. A long ground campaign could actually spawn a leader, renowned for their heroism during the "Siege of Mars".
There may be those who do prefer the auto-pilot version, maybe create an option for those of us who have dared to dream though? Maybe a companion DLC that can be turned on or off when the galaxy is created?
If you think this might be an option, I have a ton of ideas. Generally speaking, I think it would be just taking a lot of existing game mechanics, and just providing additional representations of them.