I feel like when L.L. Zamenhof came up with these country names he should have had the roots come from the name of each country in its native language instead of using exonyms from other languages. Deŭĉo or Dojĉo or something similar.
Japan is Nihon. So maybe Nihono. Also, the language was created "To enable the learner to make direct use of his knowledge with persons of any nationality, whether the language be universally accepted or not". This basically means it wasn't created just for speakers of English. Therefore, why should all the nations names be biased towards English?
Actually, if you think about it, English is the language moving all the words around. The statement "You live in Germany" becomes "Where do you live in Germany?" (or "Where in Germany do you live?") which not only has a different word order, but also adds the verb "do" out of nowhere, whereas the most literal translation of the Esperanto is "Where you live in Germany?" which is the same word order as the statement, just with a "where" tacked on the front end.
Of course, then they can start moving the words around for effect if they want, but we do that in English too.