For flagship, just create clearly recognizable battleship, cruiser and frigate sized ship (stats comparable to other ships of same size but lower PWR/CPU) that gets +10% to shield/armor/hull when in FC/WC/SC position for every member in same fleet that is under his command, on grid and not in pod.
So in proper fleet position this ship would get:
FC pos. 0%-2550% extra HP
WC pos 0%-500% extra HP
SC pos. 0%-90% extra HP
But as fleet gets destroyed (ships become pods) then the bonus to FC goes down and flagship becomes easier target.
Flagship would have no high slots, only have “+10% HP Role bonus”, some extra ECM resists and bonus to Core and Combat Scanner Probe strength.