The goal of op. Barbarossa was the destruction of Soviet units that were deployed at and near the Soviet border, that is the territories of Belorussia and Ukraine (and the Baltic states since those were annexed just a couple of years prior).

Because of the hubris of the Wehrnacht caused by its previous spectacular victories in Poland and France, and because of general opinion of pretty much any western nation at the time that Soviet Union was in shambles and unable to wage a modern war, German high command planned for a short campaign and did not make the necessary strategic preparation. Namely, Germany still did not switch to total war industrial organization, and did not conduct a thorough logistical preparation and intelligence operations.

Then there was the postponement of the operation start date due to German campaign in Yugoslavia and weather.

When the operation was finally commenced, the initial encirclement operations were successful: AG North advanced deep and fast, but faced relatively little opposition. AG Center made a huge encirclement in which they caught about 700.000 Soviet troops. AG South also made good progress, and even faced a major concentration of Soviet armor formations in Ukraine and defeated them in detail. Some say this was the actual biggest tank battle of the WW2, the battle of Brody. But overall, AG South was too weak for the task given and the space they were bursting into. It had just one Panzer Army, the rest were foot-mobile infantry armies.

However, even after these initial successes, the Soviets have been forming reserve Fronts and armies deeper inside their territory. Their resolve to fight the Nazis was crucial: Stalin called upon the people to fight The Great Patriotic War to stiffen their resistance and keep forming new reserves. They even relocated their entire factories behind the Ural mountains, far beyond the reach of Germany. This enabled them to keep forming and equipping new units.

Now even if German success was immense, it didn't happen without losses: the battles were bloody, attrition took its toll on men power and equipment. The further they advanced, the longer their supply lines became, more vehicles broke down or were destroyed. The railway in Soviet territory was wider than German trains, so that was a major issue.

By the time the Germans reached Smolensk, they have been fighting non-stop for a month, and there was no end in sight. Exhaustion, battle attrition, disease, etc, reduced their units' effectiveness, the Soviets were constantly counterattacking on tactical and operational level. Even if these counterattacks did not achieve their goals, it nonetheless caused casualties and messed up the timetable of German operations, some even causes Germans to retreat (yelnia bridgehead).

Even if the Germans managed huge encirclements at Minsk, Smolensk, Kiev, Velikie Luki-Viazma, etc, already a new line of Soviet armies was forming behind, while German material and manpower replacement could barely keep up, so you can imagine what that means in a long run.

The too-late operation Typhoon started with many German formations depleted and with experienced soldiers, officers and NCOs dead.

That's really a short version of the story.