In the past I've purchased a rail pass because I figured it'd be more economical but last trip we just got a couple of IC cards and just booked our shinkansen and that was honestly the best experience. The problem with the rail pass was that it could only be used on some services, and the IC card was usable on most. The most confusing thing is just figuring out which local transport companies have a slightly different network, but it was honestly not bad.