From what I've read I get the impression that Japan being more advanced than its neighbours in the region isn't just a recent thing. I've read things from Portuguese missionaries even from the 16th century that mention Japan being more advanced and 'sophisticated'. Is this correct, or am I wrong to assume Japan has been more advanced than its neighbours for the past few centuries?

If so, I'd like to know if there are any explanations as to what caused Japan to be different and be able to position itself above other countries in that region? Has the Shinto religion had any influence on Japan's progress?