I have a somewhat different take than the other answers here. The Japanese manufacturers have mostly staked out the volume market, which means they are cheaper to build and make. All of them are volume manufacturers (or at least they all try). While they do have luxury and performance models (lexus, infiniti, etc), they are mostly volume driven companies, and thus cost driven. It is an engineering and product design philosophy... Taking apart a Nissan is a materially different affair than taking apart a Mercedes or even a VW.

The indigenous German car builders have mostly staked out the higher end of the market over time. VW is really the only volume nameplate among the homegrown German manufacturers. Adam Opel (GM) and Ford are volume builders, but they are part of a different gene pool for the most part.

German and Japanese engineers are similar in temperament in many ways; Precision, consistency, repeatability, are things they have in common. But how that's expressed in their products is much different. The Germans have been conservative limits-testers forever, and their cars show these traits. Whether its the autobahn that caused them to culturally focus on refinement at speed through technical complexity, or elegance in mechanical design, their machine creation skills are impressive. With the exception of VWs mass market products, their cars are less compromised in totality, but are offered at a much higher cost (some is attributable to engineering, some is attributable to their high labor costs). Just look under the chassis of a modern Porsche or BMW, and you'll see materials you likely won't see on many other cars.

Japanese cars on the other hand, broadly speaking, are designed to be cheap to build and fast to assemble, something the Germans have struggled with for years. While mechanically reliable, many Japanese cars are built with much less formidable materials than many German cars. They are in many cases minimalist in design and manufacture. What the Germans do with 20 complex fasteners, the Japanese will do with 4 cheap plastic ones. You can take apart a door on an Audi over and over again and not likely break anything in the process. Take apart a door in a Nissan, half the parts will shatter in your hands and will need to be replaced in order to reassemble the door correctly. I've done both many many times, and seen this first hand. You can see that most Japanese cars are designed to be cheap to build when you try and fix something in them. German cars, are designed to be... well, designed I guess.

When you travel to less wealthy parts of the world, you see tons of Japanese cars. Kind of agricultural in their feeling, cheap, durable, somewhat chintzy, plasticky, basic and reliable. The American/European variants have nicer upholstery and some more sound insulation, but they are mostly the same underneath.

German cars are extremely refined. Every single part is pretty well thought out, even if it doesn't start out that way. Japanese cars on the other hand are refined only in the areas that make them reliable or cheap. The Japanese are brilliant at austerity on the whole. Ford and Chrysler have been well influenced by Japanese design and manufacturing ideals too. GM less so. The British never learned anything from either the Germans or the Japanese it seems. The French are unique, but have done well learning from the Japanese in many ways (they only do volume cars).

I think that any "benefits" German cars have is in the eye of the beholder, inasmuch as that person can appreciate the refinement the Germans inject into their products. The upmarket Japanese cars are nice as well, and offer many refinements at a lower cost compared to their German competitors. But even Infiniti/Lexus are designed to be cheap to build and fast to assemble, albeit with nicer materials than their downmarket Nissan/Toyota siblings.

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