My take on it right now is that siege ships are really only for looting. With the fixed planetary defenses as weak as they are, attacking with ship killers makes sense because after they defeat any defending ships, they'll just erase the planet's defenses, even if they aren't the strongest against planets.
I don't know if adding a command ship to each fleet has value or not, but, for now, my fleets are 300 ship killers or a couple command ships and the rest skip killers.