1). Make hotel reservations process similar to the rest of the developed world... ie, reservation on hold with credit card and hold group bookings to different level of accountability. Let me expound on this below.
2). Allow gaijins with tattoos to use onsen, as long as they cover it up.
3). Do something about TYO... limited capacity at NRT, two-airport system which is a mismatch. NRT has the potential space (provided they get rid of the last few remaining patches of obstruction around runway 'C') and excellent ground transport network, and methinks a 3rd runway at NRT would really help.
To discuss point #1 further, the current system in place is more like an honor system where you just book a room just with your name, phone# and email address. Hotels have cancellation policies, but how can they enforce it without any payment info? My Japanese sibling routinely holds down numerous different bookings for a one-night trip. Also, I've read Jpnese articles about hotels bemoaning last-minute group booking cancellations and losing tons of revenues without recourse. This was illustrated by my last trip to Sapporo where there were literally no decent rooms available for less than outrageous prices until ~3days before the date when magically all sorts of hotel rooms popped up. Raising the integrity of the Japnese hotel reservation system would surely open up a lot more hotel room occupancies.