I would highlight a lack of discipline at all levels of the Japanese army. At the top they were too involved in politics, in the middle there was too much plotting, factionalism and willingness to attempt coups as well as start wars with foreign powers. Meanwhile at the bottom the soldiers appear to have lived a rotten life and behaved poorly when exposed to civilians or prisoners.
Despite that both the German and Japanese armies can probably be fairly credited with being willing to innovate and pretty flexible in their actions.
Equipment wise the Germans were superior, along with having a better logistics system. But the Japanese could probably function on less which had its advantages.
The issue of discipline is I think the greatest factor and makes the Japanese far less 'professional'.
It depends. Certainly the Japanese enlisted and NCOs obeyed their orders to a T, sometimes even at the cost of battlefield flexibility. In the Japanese Army the individual fighting units almost always retained combat effectiveness far beyond the point where the Germans or anyone else would have scattered or surrendered. A lot of the problems with Japanese treatment of civilians and prisoners of war, like the German experience in Eastern Europe and the USSR, didn't necessarily stem from a lack of discipline but rather their racist ideology and the release pent up aggression on the defenseless. In light of this, I'm not so sure if that was indicative of a lack of discipline so much as a reflection of the military and political culture at the time.