It was something that evolved out of a different political environment during WW2. The Soviets and West were friendly during the war when the Yalta and Potsdam agreements were made that divided the city to split the burden of occupation and the prestige of occupying Germany's capital. However as the Cold War started and the West and Soviets fell out the symbol of West Berlin came to be a line in the sand for the resistance to Communism. Giving up Berlin for the Allies meant losing out the Soviets, which is exactly what the Soviets would see it as, while for the West Germans retaining part of their former capital was a prestige issue; it why Bonn way selected as a temporary capital until reunification could be achieved; had Frankfurt been selected as suggested, rather than a provincial town, then it would be the new capital and signal the commitment to a permanently divided Germany. So retaining West Berlin for the West Germans was like keeping half of a memento until it could be reunited with the other half.