Having played the original HWs when I was younger I now have the benefit of foresight to know how crucial capturing enemy ships can be. When playing the last two missions of HW1 you are faced with large Taiidani forces already in formation and on the attack. What is the Kushan doing? Asking themselves why it was a good idea to have the captured ships in their feet make 200k line to the side of the mothership instead o jumping in formation near the mothership.
Because you start every mission in military parade your fleets firepower is severely diminished in the crucial first moments of engagements. Have an additional command interface could easily fix this and allow players more control over their fleets during the campaign. It can reasonably be argued that any feet commander, no matter how much of a novice he is, would form his fleet of frigates and capital ships into a defensive or offensive posture prior to moving further in the unknown.
So I short, being able to designate 3D deployment zones for different ship groups would allow the player to react and maneuver his fleet in seconds, rather than watching as frigates and capitals that he salvaged move painfully slow towards the end of the battle.