I'll venture a couple guesses.

1) Humboldt's university reforms creating graduate education and research universities. This doesn't explain the seed of German intellectual activity as it was a relatively late development, but it does explain the institutionalization of German intellectual activity. As to the seed...

2) German was the language with the most literate speakers in Europe during the Enlightenment. For a few centuries after the Reformation, Protestant regions did have higher rates of literacy than Catholic or Orthodox regions, and Germans were the most numerous of the Protestant cultural-linguistic groups.