Japan is actually fairly safe when it comes to earthquakes. While it is impossible to avoid them (every region is exposed), most places have very good building structures that will resist most quakes (think that during the tsunami virtually no damage was done by the quake itself).
I really wouldn't plan a trip there around earthquake sensitivities. Osaka is a great hub to visit Kyoto, Kobe and Koyasan, and central enough to get to Tokyo or Hiroshima (both really worthwhile).
If anything, the only thing to be worried about in Japan is food following the nuclear disaster. I would avoid dairy products for instance, and would consider imported foods safer as there has been word of contaminated food making its way to shelves and restaurants... over 8 years ago
You cant visit Japan and not experience an Earthquake. It's part of the cultural experience! Having said that, there is probably no safer country to be in if you do as the building and safety codes are more strict than in any other country on earth. over 8 years ago