I feel the flanking option for Russia is overstated. Up to and including WWI in the east, armies tended to operate on a single axis without too many problems. The Germans even did it during their sickle cut through the Ardennes in 1940 without problems (although it certainly scared them).
In this case Germany could easily have spared a few armies to guard their northern flank while the bulk of the troops massed against Ukraine and the Caucasus in an alternative Barbarossa. Assuming sufficient supplies, they would have done even better than OTL as they would have far more fighting strength there.
While a nice open flank looks wonderful on paper, it is not easy to actually exploit in reality. The Mortain counterattack in 1944 looked good on paper but failed miserably while Manstein’s success at Kharkov was completely unexpected because unprecedented.
Having a nice open flank means your troops have failed somewhere else and are retreating. Morale will be low. Troops might not be easily available, perhaps most are already committed to propping up the broken front? What’s to stop the enemy from encircling your own troops while to prepare your flank attack? Russian armies during WW2 were notoriously difficult to re-orientate in another direction and launch into an attack. It took weeks of preparation. In 1941, they wouldn’t even have had the American trucks to help with logistics either.
If you accept the economic theories underpinning the German invasion, putting their main effort in a push towards the oil etc. would have made the most sense. And it would have been something they likely could have pulled off. You wouldn’t have the great pockets the original 3-pronged invasion created but that didn’t win Germany the war anyway.
The problem for the Germans is that they never made a proper/realistic analysis of fighting the Russians. Their entire strategy was based on defeating them close to the border and then race inland until they surrendered, as every previous victim had done. The whole endeavour was to be over in a few weeks, bar some mopping up. Not a multi-year campaign with realistic intermediate steps.
If the Germans had behaved as civilised humans instead of animals, it would even have worked. Plenty of Russians and oppressed minorities were initially happy with German victory. But by giving everyone not a German (bar a few token allies) no other choice but resistance or death, they ensured that battlefield victories wouldn’t be enough. It became a war of attrition which Germany could never win unless they secured the necessary resources. Which is what Case Blue belatedly tried to do in 1942.