Tokyo/Kyoto Itinerary

Hi! I'm really excited about my trip to Japan and I made an itinerary featuring what I hope to do when I'm there however I don't know if it's possible and was just looking for some feedback on it! One question that I have is whether I should stay one more day in Kyoto instead of Tokyo and do a day trip to Nara (or Osaka) or spend the extra day in Tokyo and travel to Nikko for a day? Also when traveling to Tokyo from Kyoto would it be possible to stop in Nagoya to see the Atsuta Shrine ( is it worth it?? ) and still accomplish what I have planned in the itinerary below?



A little background info:
-10 days in japan
-leaving september 25 and coming back on the 5 of october
-first stop Matusaka (hometown)
-second stop Kyoto
-third stop Tokyo
-First time there!!


My sample itinerary:

Thursday 9/25
-Leave SFO at 11:15

Friday 9/26
-Arrive in Nagoya at 6:05 and travel to Matusaka (Fumikofs hometown)
-Stay at friends house



Saturday 9/27
-Visit friends and family
-Visit Ise Grand Shrine (Amateratsu)



Sunday 9/28
-Travel to Gyozanen Ryokan and be picked up at 1 ofclock
-Visit Kyoto Tower or Kyoto Station
-Maybe visit sights around Ohara
-Night in the Gyozanen Ryokan, Ohara

Monday 9/29
-Northern Higashiyama
-Southern Higashiyama
-Walk in Gion + Ponto-Cho

Tuesday 9/30
-Arashiyama
-Central Kyoto
-Southeast Kyoto
*Fushimi-Inari Taisha (visit near sunset)

Wednesday 10/1
-Travel to Tokyo
-Harajuku
-Visit the Meiji Shinto Shrine
-Yoyogi
-Shinjuku

Thursday 10/2
-Visit Tsukiji Fish Market
-Asakusa
-Odaiba

Friday 10/3
-Day trip to Nikko (shrines close around 4:30)
*Shin-kyo to Rinno-ji to Tosho-gu, Nemuri-neko, Futarasan Jinji, Takino Jinja, Tamozawa Villa, Kamangafuchi Abyss ????????????????


Saturday 10/4
-Ueno
*Tokyo National Museum
-Akihabara

Sunday 10/5
-Maybe try to see cosplay on Harajuku Street
-Leave for home at 4 pm

Thanks!

Nikko is named little Kyoto for a reason. Some prefer it to Kyoto. But if you are already in Kyoto for a few days, I think you can forgo Nikko. How about stopping by Fuji?

Can't help you with Atsuta Shrine. Is on my list. If you do go, PM me your experience. Or better yet write a blog post on Japan Guide.

Ise shrine is big but still doable within an hour.

Kyoto is a small city with a goof transportation network. You might be able to spend more time depending on how fast you travel.

Tokyo schedule seems empty. How about you do one more location each day?

P.S.
Who is Fumiko?

I agree with the above - some things in Tokyo seem empty and slow - so you could in theory go to both Nara and Nikko by re-arranging your schedule a bit.
You could see Osaka as well in the evening. After the Kyoto temples and shrines close about 5PM, just zip over to Osaka. There are many sights to see in the evening. Dotonbori really comes alive at night, and if the weather is good the night view from the new Abeno Harukas Bldg. is spectacular. You can get a look at it from here:
http://youtu.be/-AyUZmGbW8g
To get more time in the Tokyo area, instead of going to near Harajuku twice, you can see Meiji Shrine, Harajuku, and Takeshita Dori on your last day (Sunday is the best day to go see it) and move Shinjuku & Yoyogi to what you have for Oct. 2nd or 4th. Both those days are pretty wide open still. Asakusa is also one of the most popular sights but doesn't take long to get through. See:
http://youtu.be/SwjnQDjwaPQ
Finally you don't give details for what you have on 9/30, but it's quite overstacked. You can pick a few places from each, but you won't be covering all those areas thoroughly at all.