If your commute would be that far it may be better to live closer to work, as Tokyo is crazy expensive to live in. I lived 45 minutes south of Tokyo and had a 1300 sqft house and it ran about $1,900 a month with utilities it was around $2,300 but I do love Tokyo it is an amazing city and has so many great things to see, do and offer as does the rest of Japan. There are a ton of Expat communities, groups, magazines, food websites, etc… for Japan that make life there a whole lot easier. Also most big cities in Japan the signs are in English and Japanese. Japanese is quite easy to learn as it is has a pretty straightforward language structure (Unlike English).
I know many people that lived 1hr 30 mins from their work and just rode the train to work. A lot of employers in Japan comp some or all of a persons train fare. I knew guys that would ride the Shinkansen(Bullet train) from 2-3hrs away and would stay in a capsule hotel during the week and ride the Shinkansen home for the weekends. If you live in a smaller city/town you will probably get to know your neighbors better and have a chance to be a part of a community. Every Japanese neighborhood has a community society/watch group that takes care of the neighborhood, conducts nightly watches, plans festivals and parties, takes care of the local shrine, etc… you'd probably miss out on this living in a mansion (Upscale Japanese apartment) in Tokyo.












