Japan in 2-3 days
This is a tough one because any trip to Japan should tick off both Tokyo and Kyoto. A couple of days isn't enough time to do both, though, and as Tokyo's easier to get to, it makes more sense to see the capital on a short break.
In 7-9 days
Spend 2-3 days gawping at the modern marvels of Tokyo before jumping on a bullet train and whizzing down to Kyoto. Roam the anicent wonders of the former imperial capital, and the world heritage sites of nearby Nara. On the way back, consider a trek to the summit of Mount Fuji if you're feeling energetic. If not, get off the train at Nagoya and take a side trip to Takayama for mountains and sake breweries.
Two weeks +
With a bit more time you can afford to get off Honshu and explore the other islands. Head south from Kyoto to Kyushu for the hot springs of Beppu, the volcanic chain of Kirishima and nightlife hub Fukuoka. Learn about resilience in Nagasaki and continue the theme at Hiroshima before heading back to Tokyo.
Alternatively, tour the mounainous regions of Japan by heading north from Kyoto to Nagano and the Japan Alps, before comtinuing to the island of Hokkaido. From Sapporo you can hike the National Parks in summer, or carve up the pistes in winter.