Berlin is the capital city of Germany since Reunification
Berlin has been the end point for more World War II games than one could reasonably count. The fighting in the European theatre didn't come to a close until after the Red Army sacked Berlin. In the Original Call of Duty for the PC the final mission involved Russian soldiers storming the Reichstag (the parliment) for instance.
Berlin has also been an important city because of it's importance in the cold War. During the War the city was divided in two by the Berlin Wall which the East German government put up to prevent East Berliners from crossing the boarder into West Berlin and the more prosperous West Germany. It was therefore also the spying capitol of the world for nearly 3 decades and it made for a sexy destination for a videogame when those conditions were afoot.
Since the end of the Cold War Berlin has gone from being a global hotspot to just another ancient European city. It's seen it's fair share of rock concerts and autoraces modeled on it but it just doesn't have the magic anymore.