The current problem the US Navy has is power limitations for electricity generation. Modern technology require a lot of power as the ships get more and more computers. Add to this the lasers and railguns in development, and you have some really hungry ships. While the nuclear powers ships can produce a lot of power, the older ones lack something. Either a large enough power generator, or their wiring is insufficient for the loads needed. The recently commissioned USS Zumwalt. and the new Ford-class carriers should have the power requirements for the new weapon systems, and the Fords will have their decks designed the handle the engine blasts of things like the F-35C.
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