I don´t know much of this subject and haven´t found anything that sheds much light on the subject, but it seems that the air defense of the Soviet capital was given very high priority, so I hope that by starting this thread someone with knowledge of the subject can enlighten me (and that Librarian will join in with an essay on the work of a certain mathematician who developed a system of Flak-defense fro Moscow 
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I read a personal account of a German bomber pilot lately. He reports that the air defense of Moscow was generally underestimated at the beginning of OP Barbarossa.
Field Marshal Kesselring told the crews that there was no comparison between missions over London and Moscow.
Over Moscow no enemy night fighters, no heavy flak, no barrage balloons had to be expected. All this turned out to be wrong though. The German vet writes about numerous AA batteries in and around the Moscow urban area and an overwhelming number of AA spotlights never encountered before.
Another interesting thing the German pilots experienced was the fact that over Moscow barrage ballons were floating at an altitude of 4500 meters (~14800 ft.), the max. altitude over London was 2200 meters (7200 ft.).
Because of the weak winds at Moscow’s intercontinental position the Soviets were able to let their ballons float that high without the ropes tearing.
The only “bright spot” the German crews reported was the fact that Soviet AA didn’t fire that accurately in 1941 like the British ones.
Additional info: German bomber crews counted about 500 spotlights in and around Greater Moscow.
Nocturnal impression of Moscow, July 1943:
