The Germans saw Crete as an important target for conquest. Perhaps the primary motivation was to rob the Allies of an airbase within easy striking distance to the Rumanian oil fields. Crete was also relatively close to the new battleground in Cyrenaica. Since a purely naval assault of Crete seemed too risky, due to the concern about the Italian navy, an airborne assault seemed appealing. They had successfully used airborne troops in Holland and against Corinth in Greece. They could combine that with ferrying troops and equipment to Crete from Greece using small ships. They did not need to solely rely upon paratroops, because they had the ability to ferry troops using Ju-52 transports, if they could secure the necessary landing fields.
The British were concerned about defending Crete from an airborne attack, given the recent successful use of airborne troops by the Germans against the Corinth canal. The concern with holding North Africa against attack that was now commanded by Rommel was the primary concern. The primacy of that effort meant that insufficient forces would be available for defending Crete. This is based on the account in Vol.II of the Australian Official History.