Just got back from two weeks in Tokyo after a 5 year absence. Good Lord....the city has experienced some serious changes since I lived there from 1997 to 2006.
First of all, tourism has SKYROCKETED! There are gaijin all throughout Shinjuku and Shibuya. When I lived in Tokyo, you could pretty much go to any neighborhood in Kanto (except for Roppongi) and not see gaijin. Seriously, I could go 4 days without seeing a white/black face.
Case in point, the Golden Gai district near Kabukicho. Back in the day, you could stroll through this area at night and only see Japanese people. Went there last week and EVERY PERSON I saw walking around were tourists. Really kind of sad. Tourism is really having an impact on Japan.
Went into a kaiten sushi place in Shibuya, a place I used to go on occasion twenty years ago. Went in last week twice, every person in the place was foreign. Might as well been in California. At the check out, the sign read '4 Stars on Trip Advisor'. Ugh.
So, my recommendation for newer travelers to Japan: try to NOT go where your guide book recommends. Only briefly visit the touristy places and then try quiet, off the path neighborhoods. Roll out to Kanagawa or Izu or someplace and escape the tourists.