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A variety of things, including design and supply issues (joked about in the audio commentaries of the prequels by Lucas) which are also spoken upon in the novel Death Star. It also has to do with political machinations, as Palpatine still had to deal, to a limited extent, with the Imperial Senate and objectors to the Death Star (and other large expenditures such as the Executor-class Star Destroyers) and its enormous price and manpower requirements.
By the time the second Death Star is built, the senate no longer exists, design flaws had been worked out, and Palpatine could easily justify the Death Star to counter the "threat" of the Alliance (despite the fact that he did not see the Alliance as a major threat).