I would personally like a Sins of a solar empire kind of fleet command ui but with improved 3D capabilities. For instance Sins takes place in a 3D environment but only provides 2D command options leaving the third dimension entirely up to the AI. I would like to be able to control the third dimension aspect with 3D commands. This could be done by selecting a location in 2D then using the mouse wheel to scroll up and down in the third dimension. Then (for example) selecting a ship or group of ships and holding another key would allow for X/Y orientation selection then another for Z axis orientation. The ability to take command of an individual ship or even a fighter to then take part the battle you have set up in first or third person would make this basically a dream come true.

If you want to play something like that right now, Void Destroyer is pretty much exactly what you just described.