Reading the posts on this forum over the last couple of years, it seems like a lot of it is pretty simple.
- Make immigration faster.
- Easier to get a SIM card.
- Easier to get card subway/train card (or Suica/Pasmo)
- Improve transport into the city (faster from NRT, more direct from HND)
- Let travelers know you can easily buy Narita Express and Skyliner tickets from the machines in English
- Cheaper taxis to/from Narita (allow Tokyo taxis to pick up return fares at NRT)
- Allow ADD meds for kids traveling with families (this restriction probably keeps 50% of US affluent families out of Japan)
To me the other big things are:
- Train the hotel/resort industry to be more flexible (big +1 on freccia's comments)
- Make the country more beautiful by putting the power lines and poles underground.