Generally I just kit out a Cargo ship with engines and sensors and have it follow my squads. Ala AWACS

You have hit on the right idea in the need for a command/sensor ship. However, your implementation is inefficient. Your fleets should use their maximum available logistics to stack fighters not some useless (for combat) sensor vessel. Also, since the ship only serves as the eyes of the fleet, it only needs to have the speed to keep up with them and the largest range possible. For this purpose, the majority of people use cargo vessels. They are cheaper than medium hulled, and most importantly have the most room for sensors and engines. Since they are accompanying your war fleets, their long sensor range allows them to give your fleets a large heads-up of enemies so that your fleet can defend them. Keeping it seperate from your fleet allows you that one or two extra ships that can make all the difference.

Too bad GC2 does not have tactical modules for ships.

Proposed modules:
Command center - would increase firepower by X% for all ships in the fleet.
Targeting center - would increase accuracy (by reducing attack number spread) for all ship in the fleet
Sensor scrambling - Reduces sensor range for all enemies while trying to detect fleet.

These modules should be large and costly but should make a well-planned fleet more difficult to defeat than one that was cobbled together with whatever ships were at hand.