Star Trek: Birth of the Federation was a bit clunky and had some shortcomings, but it also had some good points, one of which was a map control feature that I hope the GC3 team might consider: allow a group of ships to engage in missions such as 'interception' which will automatically engage any hostile units that come within their range (range being how far the units can go in one turn). This differs from, say, 'auto-attack' in that the units won't go across the entire map (as they would in GC2) when a freighter enters the sensor range of another vessel.
This can reduce the tedium of having to keep checking vast stretches of a map to see whether any enemy units are trying to sneak through your front lines. Of course you'll have to see them (they'll have to be in sensor range, and I dunno if there's a possibility of stealth coming into play).
I'd love it even more if this could also contribute to map control when at war ... when at war, your units should be able to push back the 'border' of the enemy you are at war with if they are unopposed.