Carl von Clausewitz in his book "On War" extensively analyses the military genius of Frederick the Great, among others. There's also another great book I've found interesting, "Frederick the Great" by Schieder. His fame comes from his many great and often spectacular successes. Also, his was very intelligent and well-spoken and was able to impress many other military theorists in his time. He won most of the battles he fought. His troops were famed for their good discipline and high morale. He was often able to beat numerically superior forces, inflicting great losses on the enemy with comparably low losses for his troops. The Prussian Army became one of the most fearsome armies in Europe under his leadership.

He invented many military tactics that were quickly copied by other European powers when they saw how effective the Prussian Army became. He put great emphasis on maneuvering, and he often managed to appear exactly where his army was needed, often catching the enemy by surprise. His most famed tactic was arranging his army in an oblique manner (imagine a right triangle, with the hypotenuse facing (edit: away from) the enemy). They'd then attack together and quickly overwhelm one of the enemy flanks, then moving to encircle the rest of the enemy forces.

The oblique formation required great discipline and mobility. Frederick was one of the first rulers to implement regular and intensive military exercises to perfect his army's coordination and steadfastness. As part of his enlightened state, he also gave great support to the enlisted and veterans. Prussia had the highest quality uniforms, the best healthcare and good wages for the soldiers. Veterans had very good opportunities to work in the government after their service. Many of them ended up teaching in military colleges and training new soldiers, expanding the Prussian military nobility.

Frederick the Great's legacy heavily influenced the Prussian and later German military in the centuries to follow up to the end of World War 2. His theories and innovations were the basis on which Bismarck managed to unite Germany, and on which the Wehrmacht developed their Blitzkrieg.

So to answer your question in short, it was the innovations he brought, his successes on the battlefield and his rhetoric when it came to military theory, all combined.