I concur with
@mdchachi: buy Shinkansen tickets at the station (cash or CC) and use IC cards (Suica, Pasmo) for local transport. Some regional bus lines issue their own IC cards, but you can also pay in cash. Suica can be used across the Greater Tokyo area (JR and metro), on JR East lines, and in other cities like Sendai, Niigata, Osaka, and Kyoto. They are also compatible with IC systems such as TOICA (JR West), Manaca (Nagoya), and PiTaPa (Chugoku, Kansai and parts of Chubu).
We are an affiliate of
Japan Experience, which sell JR Rail Passes: 7-day tickets for 332 € and 14-day tickets for 531 €. Depending on your itinerary, you might still save money with one of their passes.