Well, the way I've heard it justified is that the first DS took years because of prisoner riots, rebel sabotage efforts, supply issues, design and construction issues that had to be hammered out, and having to drain manpower from building to keeping the thing safe from attack. The second Death Star had all of these problems worked out from the trial and error of the first. Plus it was built in total obscurity and the rebals did not know about it so there was sabotaging efforts made.