Nuclear command makes the game harder :
On the destruction of the Command Centre , All , i mean , ALL fabricators are gone forever
ARS and research centres are also destructed on the destruction of the CC , which means that....... well , you know what
that means that the Nuclear CC option should be used with care and not carelessness , and should be attempted only if you are prepared to use your basic three(or four) ships and know how to use them efficentally
TRIPLE EDIT : also , Nuclear Command doesn't cut off supply , it only cuts off supply when the planet is in pieces