The unpreparedness only really affects the first few weeks. After the initial victories the Soviets were able to attempt proper defense against the Germans but met with failure. The Germans had just had 2 years of practical experience which they applied ruthlessly. Morale was high, low level initiative was high, and the tactics and forces available were right for the initial attacks.
The eventual Soviet victory wasn't so much anything to do with their economic system or industrialization but in that they simply learned how to fight modern war. Defense in depth, deception operations, the massive use of simple but extremely effective anti-tank mines and anti-tank guns as well as the proper use of armor in achieving and exploiting breakthroughs. All the while they wore down the German armies which became poorer and poorer in quality and quantity throughout the war despite the influx of 'Wunderwaffen'
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