I have visited Japan regularly over 10 years and lived and worked there.
Its a fascinating country but understand it can be a tad strange and very odd for many people. and the food can be a challenge for some, getting around can be fantastic and clean efficient.
But there is so much to see from tropical beaches to snow covered mountains with everything in-between.
People either love or hate Tokyo, and yes a lot of it is just skyscrapers and busy busy busy, but you have to scratch more than the surface and find lots to do/see.
I have felt many small tremors but more so during the tsunami, we were living in Kyoto at that time, but was more worried about the nuclear reactor and the problems that could have been. Its part of life and you will probably not feel anything.
Most visitors visit Tokyo, great shopping (depending on what your after), some bladerunner esk neighbourhoods, Kyoto, Nara, Miyajima , Fuji, Hiroshima, Nagasaki...plenty of castles, ancient sites, hot springs (onsens) and so on.
If you post more what your looking to know about feel free to ask and I will try to give info.