As a native English speaker, I say "When does the bus arrive" is a better equivalent to "Wann kommt der Bus?". Germans speaking English use the present progressive too frequently. Personally, if I were waiting for a bus that appeared to be late, I would say "When is the bus supposed to arrive/come?"
I'm not exactly sure. All I know is I saw ankommen used in Rosetta Stone in relation to time. Ex: ,,um wie viel Uhr kommt der Bus an?". So perhaps you use it when asking for specific times? RS doesn't exactly explain anything, but it works well as a partner course to Duo ^^
You would seem to be using 'is' as a helper verb, which is not correct (excepting in the case of continuing verbs). Is is its own main verb and should not be paired with come. Does on the other is almost always a helper verb and is paired with a main verb, like come, in a question.
This might be an AE vs BE thing. People just do not say "when is the bus due" here. Good, proper American English would be "When does the next bus arrive?" Or you might say (especially if it appears to be late), "When is the bus supposed to arrive?" You might also hear "when is the next bus?" (very informal).