Second to English, German seems to be the most popular foreign language in anime. You see it in titles, names, and even quite a few characters are of German descent.
For example, many characters in Shingeki no Kyojin appear to be German/have German names and there are a lot of German references. Elfen Lied is also German (translates to "elf/elvish song").
Is there a reason for this?
Historically speaking, Germany and Japan have been on friendly terms since the 1930s (and even before), due to their shared militaristic ambitions just prior to the second world war (which led to their Axis Alliance).
After the Second World War, the economies of both nations experienced rapid recoveries; bilateral relations, now focused on economic issues, were soon re-established. Today, Japan and Germany are, respectively, the third and fourth largest economies in the world, and benefit greatly from many kinds of political, cultural, scientific and economic cooperation.
As a result, there is a lot of cross-cultural sharing, which is why you see a lot of German outside of just anime as well (for example, the Japanese word for part-time job (アルバイト) is based off the German word for work (arbeit).
From the perspective of someone from Japan, I suppose there are some reasons.
First, the saturation of English names. Because there are quite a lot of anime/manga contents in Japan, it is really hard to find a new nice English name for a new character. One handy solutions is to pick a German name.
Second, the ease of pronunciation. Because Japanese language has only 5 vowels: "あいうえお", some European names are a bit hard to hear and/or pronounce for Japanese-speakers, though most German names are not really hard to pronounce.
Finally, Japanese just love Germany. They (we) have learned many things like constitutions, medicals and chemicals from Germany. They also love German products like BMW automobiles, artificial hearts, etc. and believe Germans are hard-working, honest and industrious. (Personally, I also rely on German middle-wares).
I guess past military relationships between Germany and Japan don't make Japanese love Germany, because Japanese regret WW2 and grieve what happened in Europe. Years ago, a Japanese comedian said black jokes which affirm the Axis on TV (of course, he was just joking). After that, he was heavily criticized and had to apologize in public.
Anyways today's era is wonderful because we all can talk about anime and manga here, isn't it. See you. ;)
This may supports your theory that an old affection for German ideas exists in Japan.
As a lawyer, I can add that the Japanese civil law is based on German law to a significant extent. During the late 19th century, Japanese officials planned to westernize. As a result, they established a strong scholarly exchange between the universities of Japan and Western Europe. After the first attempt to adopt a French inspired system in 1893, Japan enacted a civil code in 1898 in the German fashion. Just imagine, they voluntarily dropped core aspects of their legal tradition. This does not happen often in world history! I guess they were totally fascinated by German system... and probably by a lot of other things, too.
From a German POV:
Shortly after the opening to Japan in 1853, the Norddeutsche Bund, a group of several Northern German countries (including Luxembourg) that was the pre-organisation of the late German Empire tried to make friendship treaties with Japan like other Western states. Japan said no because the confederation was quite weak. They made a treaty with Prussia though and started to have a scientific exchange with it.
Seeing the Prussia and the German states fight in several wars and at the end becoming united made them think of the new Germany Empire as a militarily strong country and so, when they went to Europe and America to learn, they also went to Berlin. The university system, school system, a lot of teaching books for medicine and other sciences, the constitution in the year 1889 and, of course, the military was inspired by the Prusso-German system and advised by German-Jewish advisors.
In WW1, Germany and Japan fought on different sides because Germany tried to gain power in China. There were German war prisoners in Japan, but they were treated relatively well, which lead to some of them staying in Japan even after they were officially released (because in Germany, there was a financial crisis and a very political insecure situation at that time.)
Then WW2 came and they became friends again, and since then, Germany and Japan were more-or-less friends. A lot of German cities have Japanese partner cities, and since both countries had to build up their country, society, and economy again, there was a lot of economical exchange in the following decades. :)
I think it also has something to do with the mentality of the countries; both have a strong working ethos, a relatively strict social system that builds on politeness and certain aloofness. I suppose that these similarities paired with the exoticness of being Caucasian make the stereotypical German interesting and cool for the Japanese that write the manga. Not to forget that our language is just really badass and beautiful and awesome. ;)
German used to be the lingua franca among scholars in Japan, just like Latin has been in Europe.
So when you want to give things a scholarly vibe in the West, you use Latin and when you want to do this in Japan you use German.
But unlike with Latin, there's actually still people around that actually speak German, so you can have German characters in a modern settings without having to use time travel.
In the old days Germany had al lot of fancy elite schools for the rich. This is might be the reason behind all of those rich school elite anime with Germans in them. In general I can only speak for myself and some other Germans. We love Japanese culture and this might also be the case for some Japanese Manga autors
this might be helpful
