As a summary of our trip in 2013 here is our day to day summary
Day 1: Tokyo- Land at 9:30am Narita airport- head to Jimbo-cho to check in and then visit Ueno park, explore Jimbo-cho in the evening
Day 2: Tokyo- Asakusa Senso-ji temple, Skytree, Yasukuni shrine in the evening
Day 3: Tokyo- Ghibli museum, Senso-ji at night
Day 4: Tokyo- Harajuku, Meiji Jingu and Yoyogi Park, Yasukuni shrine when still open
Day 5: Tokyo- Imperial Palace gardens
Day 6: Tokyo-Enoshima, visited Enoshima island and Kamakura Daibutsu
Day 7: Kawaguchiko- visited Chureito Pagoda, Kachi Kachi ropeway and Kawaguchi-ko lake
Day 8: Kawaguchiko- K’s house Walking and Bus tour around Fuji Sengen shrine, Fuji 5th station, Wind cave, Ice cave, Aogigahara, Motosu Lake, Oishi Park
Day 9: Ito – Izu peninsular: 100 year old onsen at K’s house Ito, travel to Kyoto (arrive 10pm)
Day 10: Kyoto- Kiyomizu dera temple complex, Fushimi Inari Taisha
Day 11-14: Tokyo- Ueno park, shopping (trying not to melt)
My Nihon 
There is no doubt all of these are the best places for enjoying the cherry blossom festival there. I will try to go there one by one but now I am taking a cherry blossom dc.
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