I think staying overnight at a temple in Koya-san and having an early morning stroll through Okunoin would be very memorable.
You might also consider the scenic mountain route to Tokyo from Kansai... head to Takayama and see the Hida Folk Village, then spend the next day hiking in the Japan Alps area of Kamikochi, which is beautiful, and then go on to Matsumoto and see the famous black castle there before heading on to Tokyo.
Hida:
Kamikochi:
