I like this poll but it'd be nice to narrow it down a little,
Are we talking about for visiting, living, the food, the people, partying, the sightseeing etc?

I have been to all off them, and i think each one has its one beauty. Its so hard to deside:
I could go for Hokkaido for its beautifull nature and awesome people,
or i could go for Honshu with its huge megacities and Japanese popculture,
or how about Shikoku with its beautifull little temples, surfing spots and getaways?
I also liked Kyushu with the big city with a little twist (Fukuoka if compared to other Japanese citys) and bathing in hot sand on the southern tip.
And last but not least Okinawa with its alternative lifestyle and food and many small places to get away to.

Hm....
I think i´ll go with Honshu, because it covers most of it. The beautifull nature in the north (autum hiking in Tohoku is awesome), the megacity Tokyo, all the temples in Kyoto, recent history in Hiroshima and beautifull places like Amanohashidate, Miyajijima and Matsushima!

But every iland has its own flavour, so i recommend to find the right one for you or just go and see them all : )