Possible Clues:

• Honshu location: Tokyo perhaps?
• Noncapital city whose name means 'capital city'
• Home of many Shinto shrines (... + first 2)
• Climate change protocol city
• City near Osaka
• Capital of Japan from 794 to 1868
• Former world capital whose name means 'capital city'
• Nintendo's home city
• Tokyo's wrong Japanese city
• Former capital of Japan (and anagram of the current capital)