Of course i am not all suggesting that Germans could have managed to take ALL of Russia. I am just analyzing Moscow from a military point of view, hub of all communication and road networks in Western Russia, seat of the government at that time. Generals were all of it since it was better to take it and base defence around it rather than staying in the open during the winters, which they eventually did and suffered.
The point whether Russia would have fought to the last man etc, is, in my opinion, debatable (Keeping in view Stalin's excesses against the locals, purges of Soviet Armed Forces 1937 onwards and some other factors). The cooperation, with Germans, of army officers like Gen Vlassov, of communities like White Russians and Cossacks (of which in the end a whole Corps was fighting along side Germans), they all seem to suggest that Russia was NOT strong as a Nation.
Your point regarding the supply system of German army is valid. Apart from things you highlighted, German infantry was still mostly horse-drawn instead of motorized.
Overall, one can conclude that the German army, as a whole, was not capable for going somewhere deep like Russia.