I've no idea what the scuba diving is like, but I know that it's a great place to visit, because I used to live there! There is lots of lovely coastline, so I would have thought that it would be quite good for scuba divers.
The food is great, and some of the places to stay are great. There are some really nice temples to see.
Japan is the sort of place that is great for a holiday if you are interested in learning about other cultures, and willing to make a bit of effort.