Firstly, make Nuclear submarines able to carry and launch Missile units the same way Aircraft carriers are able to use aircraft. This is pretty much their entire purpose in real life, and should be reflected in game. 


Similarly, after completing the first Nuclear test project, cities should gain the option to produce Nuclear bomb units without the Rocketry or Missile  technologies. Airfields should be given an addition set of slots for Bomb units, and one is consumed when a Nuclear strike order is given, but instead of having the additional combat strength like Nuclear missiles do, they rely entirely on the Bomber delivering them. Their weight could  possibly give -3 Combat strength to the Bomber for balance, as they would be easier to counter with defensive fighters.