Crete really was a bloodbath for the Fallschirmjager, but they also suffered heavily in Greece (at Corinth) and in 1940 in Holland. Eben Emael and Oslo were the only really successful airborne operations, and both benefited by being launched before war was even declared. By 1941 it was obvious that surprise wasn't likely to be achieved anywhere important, and realistically, there simply weren't very many scenarios where an airborne assault would be all that useful. Maybe in the Perekop/Kerch in 1941, and maybe they could have prevented some demolition at Maikop in 42, but realistically in 1941/42 the 7th flieger had only a handful of squeeze bore anti-tank guns and unlike Crete, the Soviets had lots of tanks.
Malta was probably the last chance the Germans had to use their airborne forces for a decisive operation, but fortunately for the Allies Rommel wanted nothing to do with it.