I would say the two most important factors would be time, and the economy.

Nazi Germany simply had less time to build their navy. Technology may have allowed for faster ship building but the types of ships being built had also advanced. Assuming that Nazi Germany began building in 1933, it only had 6 years to build up a navy before it had to also build replacements and repair damaged ships. Pre WW1 Germany began its plan to match England's Naval Power in 1898, 16 years before the war broke out.

As for the economic factor, Nazi Germany was building a Navy following the Great Depression, so its economy was not stellar. After reunifying in 1871, Germany underwent a massive economic improvement, specifically due to the fact that it was finally industrializing. Capabilities and resources were growing rapidly and Germany could sustain its ship building in a way that Nazi Germany could not.

I'm sure that there are other factors as well, these were just two that I could think of initially.