IIRC he had a high/respected rank in an army

You could say that, since it was Napoleon himself.

looked at the battles on Wikipedia though and Napoleon outnumbered his opponents in almost every battle, sometimes by a ridiculous margin, so it doesn't seem that special.

Well that's the thing. When you look at the campaign as a whole, the numbers were relatively even. When the Austrians invaded Bavaria in April 1809, they had a huge army, 180,000 strong in six army and two reserve corps*, while the French corps were divided into dispersed cantonments throughout much of Germany. Moreover, Napoleon had invaded Spain with a powerful army, which included most of the forces whose training he had personally overseen and whom he had led to victory after victory. As such, he had to improvise an army to meet the Austrian invasion. The force Napoleon pulled together to respond totaled some 175,000 men in five army corps plus a couple extra divisions. Many of these troops were new conscripts or German allies, whose quality varied from good to quite mediocre. The vaunted Imperial Guard was not available for these battles. His situation was made still more difficult when his chief of staff Berthier, temporarily commanding the army in Germany ahead of Napoleon, issued the wrong orders, which left Davout's 3rd corps stranded east of the rest of the army.

This raises the question of why the Austrians were so outnumbered in the individual engagements that made up this massive running battle. Simply put, Napoleon made better use of the forces at his disposal. He had a firm plan in mind, but was able to adjust to new events and information. He acted decisively, making the most of the time he had. He had the confidence in his army to demand the utmost of his men; elements of Davout's corps marched 150 km and fought four major engagements in a mere five days. Napoleon stayed one step ahead of Charles throughout the battle, getting results from local superiority and exploiting them to the greatest advantage.

One big aspect of this is Napoleon's operational economy of force. While most of the Austrian army advanced south of the Danube, they had originally planned to march down the Main in central Germany alongside the Prussians, using Bohemia as the staging point for their invasion. Prussia's unwillingness to join the fight scotched this plan, but two of the Austrian corps on the right wing (I and II), roughly 50,000 men, remained in Bohemia. When they invaded Bavaria, they remained on the north bank of the Danube until late in the battle. Napoleon only had a couple thousand troops on the north bank, while he focused everything else on defeating Charles's on the south bank, giving him a local advantage.

Tying into this was the resilience of the French army. The main crossing point over the Danube, Regensberg, was stoutly defended, and the bulk of Davout's 3rd Corps was nearby. Having its own infantry, cavalry, and artillery, being led by experienced veterans who had fought together in numerous campaigns, Davout's corps occupied the center of the Austrian army (III, IV, and I Reserve corps) for much of the five days of battle, escaping its isolated position with heavy fighting on the 19th of April. To the north, it wasn't until two Austrian corps converged on Regensberg that this isolated outpost was finally captured on the 20th, by which time events had overtaken the left wing. Because French troops controlled Regensberg and could fight outnumbered for a considerable period, the Austrians were unable to make full use of their numbers.

While Davout and the garrison of Regensberg consumed Austrian attention for the better part of two days, Napoleon was on the move. Because of his strategic skill, he was able to concentrate superior forces against the Austrian left wing (about 60,000 men in V, VI, and II Reserve Corps) at Abensberg and defeat them before any reinforcements could be sent to retrieve the situation. This victory split the Austrian left from their center, forcing a retreat to Landeshut; the Austrian left and right were now separated by 30 km. A second engagement there on the 21st sent the remnants of the left wing hurrying over the Isar, unable to play any further part in the battle.

No sooner had Charles united with his right wing than his left retreated. He planned another offensive against Davout, employing his right and center, while Napoleon was preparing to strike his own decisive blow. Having driven off the Austrian left, Napoleon turned north to envelop Charles's flank on 22 April. Combined with the frontal engagement against Davout and a Bavarian division, this completed the defeat of the Archduke's army. The next day he drubbed the Austrian rearguard, clearing the angle of the Danube and Isar of the last Austrian units. He then raced down the Danube, capturing Vienna just one month after leaving Paris for the campaign.

The Austrian loss in all these engagements was more than twice that of the French. Recovering quickly from operational surprise, the French moved nimbly and confidence while the Austrians dawdled. Napoleon's intelligence was flawed; on 20 April, he believed he had defeated the main Austrian force instead of just its left wing. However, he was still able to adjust to new information and act accordingly. In war, it often takes exceptional talent to achieve even mediocre results. Given the parity of strength, the improvised nature of his army, and the speed with which he turned a retreating army into one parading through the enemy capital, I think Napoleon was justified in considering the running battle of April one of his best campaigns.

*I'll also note that the numbers on the wiki are contradictory; you'll note that the wikibox says there were only 42,000 Austrians at Abensberg, while the order of battle section gives them 76,000. Part of this is being selective about what counts as participation in the battle, since many units remained in reserve or otherwise inactive during the fighting.