I was in Tokyo in 2014. Here are a few quick observations:
1) How Tourist-unfriendly the city is. There are various different metro lines run by different companies that aren't interconnected. Get on the wrong one and God knows where you will end up.
2) Half of the ATMs don't accept foreign cards. I've used a foreign card at a 711 up in the mountains in rural Taiwan. That was fine. But not in Tokyo.
3) Lack of English proficiency. In Seoul, Shanghai, Taipei, Hong Kong, I'd say at least half the people under 40 can speak passable English. Not in Tokyo.
BUT despite all that it's very, very clean!