Ok, I know this is a rather old-ish thread, but I really love rts games and I would love it if an rts feature could be implemented. So, that being said, maybe there could be like a holo table on your capital ships or something that gives access to your fleet? Or maybe just an option on your GUI that says 'fleet control' or something, that way they don't have to add a whole new block to the game. But it could give a top down view of 9 sectors in a square, much like the galaxy map, with the one that you are in being the center, with all the ships in those nine sectors as little arrows facing the direction that the ships are facing. With allied ships being green, fleet ships being brighter green, enemies being red, and neutrals being blue.
You could click on your fleet ships and give them 4 commands, attack (click on the ship you want them to attack) move (click where you want them to move), follow, (click on the ship you want them to follow), and idle, which is self explanatory.
Though a holo table would be pretty cool...
Anyways, don't know if anyone cares or not, but those are my ideas.