We had a lovely time on Millenium and Japan is gorgeous. We did excursions to Hiroshima and Nagasaki (peace memorials), Kyoto, South Korea Tea garden. We did more ship excursions than we would normally do as we will probably never get to Japan again.
From our hotel we took a train into central Tokyo, was really easy to do. (Hotel was Grand Nikko Tokyo and was lovely.
If you’re going with Imagine cruises you get an excursion to Mount Fuji and Bullet train included. You also get drinks package, WiFi and tips included.
Hope this helps. Would have replied earlier but we’re just back from a Canaries cruise to escape the wet weather.