Hitler hated Berlin. He hated its cosmopolitanism, its freewheeling bohemianism, its messy vitality, its insolence. It was the only major city that the Nazis failed to win in the 1932 elections. It was long a center of left-wing support. That's why all the big party rallies were in Nuremberg, and not in Berlin. Hitler planned his revenge on Berlin as obsessively as he plotted his revenge on everything else in his long list of hatreds.
Hitler wanted to effectively destroy Berlin, or at least a very large part of it, and rebuild it as "Germania," the capital of his global empire after his war of conquest was complete.
"Munich was the birthplace of the Nazis. Hitler was popular there, while Berlin had always been a leftist city. In fact, Hitler hated Berlin - it was Goebbels’ idea that the new government should set up in Berlin. As a result, the city was damaged by air raids, and especially by the Battle of Berlin. After the war, Berlin suffered once again when she was split among the allies and consequently the divided by The Wall. While Berlin paid for Munich’s mistakes over decades, Munich prospered – and still prospers now, while Berlin, the great building site, is in ruins. (posted in 2010)
As to Kristallnacht, if you would visit Hitler's first concentration camp, Sachsenhausen, located near Oranienburg, just north of Berlin, you would learn that for the first two years after it was opened in 1936 (prior to Kristallnacht, in November of 1938), there were no Jews there, but rather Berliners who were journalists, priests and ministers, academics, artists, homosexuals, trade unionists and communists - the cream of the city's intellectuals and political activists.