1. German General Staff/prussian military traditions & almost myopic focus on tactics, troop training and operations
2. focus on mobile warfare, the creation of the panzer and light divisions. This is along with the tendency to concentrate development in the top 20% (mobile units).
3. No strategic air force or surface navy of note; a larger share resources instead shifted to developing ground force and tactical airpower in service of ground forces.
4. German military was a 'one shot'/ "shop window" force that was structured around short wars of movement rather than long attrition battles (like the Red Army). They invested a time and resources in divisional training which meant that most of their capability was in intangibles/capabilities rather than durable systems and production. They had to win fast or not at all.
But this is normal for a peacetime army; keep the officer cadre intact and recruit/conscript as need arises, rather than keep a whole army sitting around doing nothing. The Red Army certainly did this in the 80's at least, and the US is similarly top-heavy now, despite its degree of activity.
I find the German Army to be the best in 39-41- as it fought in wars that it was designed for. The greatest operational weapon they fielded was Fliegerkorps 8 and Panzergruppe 1 to 4. FK-8 may have set the standard for aerial-ground support in WW2. Their infantry divisions were also pretty solid. By 42', their capabilities were much deteriorated but they had some left for the summer offensive and surgical set-piece operations. By 43' they were in irreversible decline and basically fell apart in the summer of 43' with the infantry arm collapsing before and during the battle for the Dnepr.
44-45 there is not much of note left in the German military except the 'GD' division, which was an elite that was kept up to older standards. Without high capability units, they can't do much.