Ok, I am going to bring up that Gratuitous Space Battles model, again...
In GSB, you set the formations of your fleet beforehand, but then the battles are autoresolved. GSB focuses more on balancing designs to see which combinations of systems will best augment your fleet, and replaying a given scenario with your different designs until you strike the best balance versus a given enemy, which really isn't that much different than the GalCiv situation. Your design choices can be influenced to a degree by what your current 'major' opponent is fielding against you, and what technologies you have available.
I'm thinking that introducing a 'formation' mechanic (optional of course) into GalCivIII could be interesting. Of course, this could also introduce some other new design choices (i.e. a point defense screening frigate that shoots any missiles that pass within it's field of fire, to protect the bigger weapons platforms), but that would be MUCH more in depth than the current model, where a ship is essentially almost soley responsible for it's own defense.
When a fleet is formed, ships would be autoassigned to a 'default' formation/position, but a player could open a window and shuffle ships around, so as to designate the formation ships form into when entering a battle.
Of course, no formation survives contact with a similarly powered enemy, so once ships enter the fray formations will begin to disintegrate, some ships might lose some speed so they can't keep up due to damage, etc.
GSB really is rather enjoyable to watch, and you can 'fast forward' battles as well to complete them faster. I'd love to see something along those lines in GalCiv III. The 'whirling dervishes' in GalCiv II are kinda cool to watch, but it could be much cooler...
In my book, what'd be real cool would be if Positech and Stardock could come together and play off of each other's strengths, i.e. Stardock provides the universe, tech progression, etc, and Positech provides the space combat model. But I'm sure both companies like keeping their own games 'in house'. I can dream though...