First timer here, going to Japan at the end of Oct for 15 days. We're 2 travellers, will be arriving in NRT and depart from KIX. Here is our rough itenarary...comment is much appreaciated

We're mostly into food, anime stuff; not so much on shrines and temples. There are still a few items under consideration.
Day 1 - 7: Tokyo - Hakone - Kyoto» Click to show Spoiler - click again to hide... «
Day 1 Sat
- 8am arrive in NRT T2
- NEX to Shibuya
- Check-in/drop luggage: accommodation @ Higashi-Shinjuku
- Get Hakone 2D Freepass + "Romancecar"
- Shinjuku, Shinjuku Gyoen
- Dinnenr at Omoide Yokocho
Day 2 Sun
- Visit UN Farmers Market or Ebisu Marche
- Harajuku: Takeshita Dori, Omotesando
- Lunch at Daikanyama
- Shibuya: Hachiko Statue, Center Gai
Day 3 Mon
- Tsukiji
-- 6am: Sushi Dai/Sushi Daiwa
-- 9am: wholesale market
- Asakusa: Sensoji Temple, Nakamise Shopping Street, Shin-Nakamise
- Akihabara
Day 4 Tue
- Nikko day trip
- Night stroll around Tokyo Skytree
Day 5 Wed
- Ikebukuro: Nekorobi Cat Café, Otome Road and Sunshine City mall
- Nakano: Nakano Broadway
Day 6 Thu
- To Hakone by Limited Express "Romancecar"
- Check-in/drop luggage: ryokan @ Gora
- Free and easy
Day 7 Fri
- Check-out
- Round course back to Gora and collect luggage, then to Odawara? OR
- Forward luggage, round course to Hakone-Yumoto, collect luggage, then to Odawara?
- To Kyoto: Shinkansen Hikari (~4pm,~6pm,...) or Kodama (every 30mins)
- Get Kansai Thru Pass (2D? or 3D?)
- Check-in: accommodation @ Tofukuji
- Night stroll around Gion, Pontocho
Day 8 - 16: Kyoto - Osaka - Nara - Kobe» Click to show Spoiler - click again to hide... «
Day 8 Sat - Kyoto (Central-West)
- Get Kyoto City Bus All-day Pass
- Nishiki Market
- Higashiyama: Kiyomizudera, Kodaiji Temple, Eikando Temple, The Philosopher's Path
- Shopping at Shijo Street, JR Kyoto
Day 9 Sun - Kyoto (South)
- Tofukuji Temple
- Uji: Byodoin Temple, Omotesando
- Fushimi Inari Shrine
Day 10 Mon
- Arashiyama (enough time? *Activate KTP)
- To Osaka
- Check-in: accommodation @ Daikokucho
- Nipponbashi Den-Den Town
Day 11 Tue
*Activate KTP
- Osaka Castle
- Kobe day trip: UCC Coffee Museum, Kobe Harborland
- Moriya Steak House
- Still some planning left to do
Day 12 Wed - Nara day trip
*Activate KTP
- Kofukuji Temple, Yoshikien Garden, Isuien Garden
- Nandaimon Gate, Todaiji
- Mount Wakakusayama (enough time?)
- Nara Park, Shin-Yakushiji Temple
- Naramachi: Koshi-no-Ie Residence
- Night stroll at Dotonbori
Day 13 Thu - Namba (Minami)
- Get Osaka Amazing Pass 2D?
- Kuromon-Ichiba Market
- Sennichimae Doguya-Suji
- Hozenji Temple, Hozenji Yokocho
- Shinsaibashi-Suji
- America-Mura
- Shinsekai
Day 14 Fri
- Osaka Tenmangu Shrine, Tenjinbashi-suji
- Momofuku Ando Instant Ramen Museum (IKEDA(OSAKA) (Hankyu Takarazuka Line Exp.)
- Umeda: Umeda Sky Building, Grand Front Osaka, HEP, Kitashinchi District
Day 15 Sat
- Osaka Bay area: Naniwa Food Theme Park
- Check-in: accommodation @ Izumisano
- Izumisano Outdoor Market
- Rinku Town: Marble Beach, Rinku Premium Outlets
Day 16 Sun - Departure KIX