The big issues with a command ship are:
1: Making the ship system actually a decision - that's why I suggested a 'burst' device, rather than an always-on one. Though, one could go with a built-in unique hull mod, and reserve the actual ship system for something else...
2: Making the effects & limits of the system clear; this is why I suggested affecting all allied frigates and fighters - this means you don't need to try and show the player where the edge of a range-limited effect is.
However, one could also go with a command ship whose effects aren't in-combat. Imagine a built-in hullmod that, say, increased maximum CR for frigates by 10%. Or steal the idea from Starsector+ of a ship that, after a battle is over, sacrifices its own CR to restore the CR of allied frigates.
Another interesting idea might be a command ship that, when deployed, grants its side two command points (and removes those if it retreats or is destroyed), allowing for slightly more micro-managing under player control. I'm not sure if that would provide much bonus to the AI, though.