Some more random wish list:
1. ECM and ECCM be modifiable like other sensor systems. Variables such as the size of the system, how powerful it is (ie: range, rule of square), how effective it is (ie: efficiency), how hardened it is, and how stealthy it is. With a powerful but low tech ECCM being able to simply burn through even very high level ECM at close range.
^^I realize there is a post concerning EW above me, but in my defence I did not see that until I looked at the preview.
2. Laser CIWS, Meson CIWS and Railgun CIWS. I realize not everyone uses CIWS, but I love the idea of having a Laser GUARDIAN system (Mass Effect) or a railgun based Asteroid Defence System (Dead Space). Also the ability of CIWS to target fighters and boarding parties that stray too close when there are no more missiles to shoot.
3. Having modular 'slots' where the roles of certain ships and fighters can be changed. Examples include ECM pods for fighters, changing a shuttle from long-range recon duty to troop ferrying duty, or changing a ship's weapon configuration for certain missions. Sometimes I wish I could just modify a ship for one mission instead of having to retrofit the entire ship for several months.
4. More satellite equipment for ships. Orbital loaders, ferries and lighters (Ship based Spaceport), Medical lab (population growth, genetic engineering), Fighter or Ordinance Fabrication, Internal/Mobile Shipyard, Manufacturing Sections, Supply Production, GF Training (Bonus to Marines) and so forth. Having some of them work without orbiting a body would be nice as well.
5. Secret Police, Propaganda Centres, Reeducation Centres, which lower the effects of unrest, or lower unrest entirely. Military Police ground units, which reduce unrest greatly compared to other units.
6. Atmospheric Dust should lower the accuracy of future orbital bombardment, but any misses should still produce dust and hit civilian targets.