Attack and defense formations would be great.  Another idea that I had was for an auto retreat where individual ships could automatically leave the fleet and retreat if their health gets too low.  It would allow me to focus more on the battle and less time moving through the interface to make it leave the fleet and retreat.

Also could there be ability for scout ships to be cloaked when they are not moving or firing?  This would allow them to be used as you can put it on the tech tree so that it can be researched.  You can give them the ability to detect cloaked units to other scouts and maybe a frigate or two.