I went to Japan last year from Mid Oct to Early November.
I bombed a large sum of money at the Square Enix Character Goods store, but that has nothing to do with travel costs cos I shall cut that out of my budget estimation when I tell people how much I spent there.
All in, for 17 days I spent SGD3000.
During these 17 days, I spent time in the Kansai area (about 8 days). Tokyo (about about 6 days), Hakone (1 night) and around one of the five lakes around Fuji (1 night).
In Kansai, I stayed in K's House Kyoto and in Tokyo I stayed in K's House Tokyo. I found K's House to be relatively convenient and affordable.
If you are not going to do a all around Japan blitz, than a JR Pass may not be suitable for you. It costs a lot and the money can only be recouped if you take long rides on the Shinkansen, or if you take so many local trains that you don't have time to see anything off the trains.
Regional Rail passes may actually work better. In Kansai, I bought a Kansai area pass (I think I bought the 4 day one) and most of the cost was offset by the Kansai Airport to Kyoto Limted Express that I took on the first day. The 4 day pass costs 6000 JPY and a one way trip between the airport and Kyoto costs around 3000 JPY.
I had considered buying a 7 day JR pass to cover the Shinkansen that I would be taking to Tokyo, but I realised that with my itinerary, it would not be worthwhile. My friend and I were doing the "Take it easy" way. We would spend one day at one main location, e.g. Kobe 1 day, Nara 1 day. We didn't really do much shuttling between towns / cities / whatever other places so a JR Pass would really have cost us more than what we would have spent.
Before deciding on whether to buy a JR Pass, work out a rough itinerary and then estimate your travel costs. If you do a Hiroshima to Hokkaido trip, then you are all covered
Flying to Japan is so cheap now. I had to pay around SGD 1200 on my airfare. My SGD 3000 for 17 days estimate is inclusive of airfare, food, accomodation, overland travel, admission fees and minor travel. Basically all expenditure I had in Japan..... minus the spree in Square Enix CHaracter Goods Store. You don't wanna know how much I spent there!
All in, I think that it is definitely possible to have an affordable time in Japan, but if you wanna go shopping...... bye bye wallet!