The big problem for the Germans was England. The island became a giant stationary aircraft carrier. Every German ship building and maintenance facility was within their range. In order to get a strong naval presence in the atlantic the Germans would have to occupy England and that was next to impossible.
Even if the Germans would have put the Graf Zeppelin into service it wouldn't have sailed long. It would have been a prime target. Also, the Stuka's are slow and very vulnerable to AA gun fire. (8
Stukas attacked the bridge at Remagen, all of them were destroyed mostly with machine gun fire)