I guess to clarify, what did he do that was so different that caused him to be highly regarded. He had a massive nation of people that had been at war for a long time and was battle hardened. Those seem like things that could make the competent seem brilliant, no?
Difficult to answer since "great military mind" is really a subjective term with no clearly defined criteria. I am partial to /u/vonadler who has a pet theory on how to rate military commanders (originally posted in a thread about Napoleon which I can't find but here it is in another thread). If you ask nicely I'm sure he can find his original thread on Napoleon evaluated by these criteria. There is also this extremely well developed thread that goes into great detail on several aspects of what made Napoleon great, not just competent but if you want a TL;DR, here we go:
Speed. Never before in the western world had anyone moved large armies as quickly as Napoleon did. (The Golden Horde and the Roman legions might be considered equal examples). This was achieved through an increased focus on the ability to live off the land and a reorganization of the army into independent corps sized units.
Initiative. Napoleon was not just fast on the field, he also knew how to capitalize on his speed. Two notable examples of this would be; A) the ability to cut off the enemy supply lines by moving a substantial force behind the enemy, thus forcing them to either fight on Napoleons terms or retreat, also on Napoleons terms. B) The ability to utilize his forces more effectively, for example, fighting a delaying action against one army with a small unit while concentrating his forces in an attack on another army with the bulk of his forces, then turning back to the first army after the second is defeated. That kind of strategic mobility was unmatched at the time.
Organization and supply. Napoleon standardized a great many things, weapons, cannon, supplies etc, this allowed easier access to supplies. He also emphasized the use of concentrations of artillery and mobile infantry to quickly punch a hole in the enemy lines and capitalize on that. Lighter cannon meant more mobility, the average french 12-pounder was over 30% lighter than a comparable British piece for example. Again, this allowed faster redeployment of artillery and the same flexibility as mentioned in point 2.
Strategic sense. Napoleon understood well what was possible and what was not. He also had a relatively good sense of what his enemies would do in most cases (Austerlitz for example). This allowed him to anticipate his enemies moves in many cases and even when he could not, he had highly mobile reserves to adapt to the changing situation.
Seen in this way, nothing he did was truly new or revolutionary but he did refine and perfect a lot of concepts and understood how to use these changes to his advantage.