I know Berlin was the capital of Nazi Germany, but the Allies chose Bonn as the capital of West Germany. It seems obvious that having half of the city under the control of the west while the city itself was located deep in East Germany would be a major and constant point of confrontation. I don't understand why the Western Allies wanted to hold it at all.
It wasn't so obvious in September 1944 when the original occupation zones and Berlin sectors were agreed (to be modified with France's inclusion ten months later). Except for a period from Yalta to the surrender when outright dismemberment was considered, Berlin was still foreseen as the future capital of a democratised Germany, and in the meantime it was to be the seat of Allied administration, divided into sectors for convenience and to give each occupying power a base but otherwise run jointly (even if that isn't quite how it worked out).
The western presence in Berlin was thus envisaged as an element in an all-Germany administration rather than an isolated outpost in a Soviet-occupied east. And the initial signs were vaguely promising, Moscow proposing (August 1944) that the inter-Allied Kommandatura for Berlin should explicitly be subordinate to the wider Control Council for Germany, which should have gone some way to preserving the city's political unity. The arrangement yielded a free last city-wide election until reunification (October 1946) resulting in a defeat in all sectors for the Soviet-backed SED at the hands of the western-leaning SPD which had been strongarmed out of contention in the Soviet zone outside Berlin.
It was only the breakdown of east-west relations in 1947-48 and the collapse of joint government that produced the divided city of later memory: though tensions had never been far below the surface, the rapidity of the Cold War's onset could barely have been predicted three years earlier. And holding on to West Berlin was to prove a valuable thorn in the side of Nato's Warsaw Pact adversary as Europe's division hardened. The inconveniently-situated outpost turned out to have been a more than worthwhile geopolitical investment.
For wartime western policy on Germany's future, see PE Mosely, Dismemberment of Germany: the Allied negotiations from Yalta to Potsdam in Foreign Affairs 28:3 (April 1950), and for discussion of the envisaged occupation regime US Dept of State, Foreign relations of the United States: diplomatic papers 1944, Washington 1966.