twotimesadingo

Here are a few recommendations (though they may be a bit biased, as I prefer the Kansai region over Tokyo).

Not a month ago, my best friend and I embarked on a trip around Japan at the end of our semester. We started in Kyoto/Osaka, then moved southward, hitting Nagasaki, Fukuoka, Hiroshima, then Kurashiki. We then hit Kyoto/Osaka again for a few days, and went north to Nagoya, Nagano, and then celebrated the New Year in Tokyo.

That said, I honestly believe Tokyo is far overhyped. Here's the rundown: it's big. Damned, if I may be so bold, fucking big. You won’t have seen anything like it, and you wont ever again unless you go back. It's metropolitan area includes 8 million more people than the entire New York Metro area, which by measurement is far larger in area. Tokyo Metro is about 2 times the size of the next largest city, Shanghai. So, while I do think Tokyo is overhyped, I definitely think everyone should see it. The first time I saw Tokyo - and specifically, the 2 million people that move through Shinjuku station every hour or so - it shifted my world view.
Then again, I don't think Tokyo deserves a week. I'd say spend a day seeing Yasakuni Shrine, Meiji Shrine, and Akihabara (the most phenomenal electronics district I've ever had the opportunity to behold); then spend one more putzing around Shinjuku/Harajuku during the day and Shibuya at night. That's two nights. And, in my honest opinion, it's all you really need. Then again, coming from the Osaka, the shopping/dining aspect of Tokyo doesn't really do much for me.
As a side note, if you can get up around 5 in the morning or so (which may well be possible, given jet lag), you should definitely see Tsukiji Fish Market. Fucking awesome.

By saving a few days, you can make a one or two day trip over to Nagano. There's an onsen (hot spring) about an hour by bus which is also the home of over 270 wild monkeys. I'd imagine that would be fucking wild. I didn't get a chance to go there, as I was running short on money by that leg of the trip, but I really wish I had. Onsen are definitely worth a few hours, or a day if necessary for travel. And even without doing the onsen, Nagano was great fun, and one of the prettiest cities, in my opinion.

From Nagano, I would then begin maneuvering south, through Kyoto and Osaka. Kyoto is the main attraction here. As Bundy said, Kyoto deserves easily a week. Most importantly, I would hit up the Philosopher's Walk, or Higashiyama Walk (both of which include Ginkakuji - my personal favorite temple in Kyoto). The two are essentially the same thing, but Higashiyama Walk includes Kiyomizu-dera, making it a preferable day trip. However, I personally believe Kiyomizu-dera and the warren of streets at its base deserves a full day, but as you are constrained on time, this may not be possible. After that, I would hit up Heian Shrine, with it's beautiful Shin'en Gardens (featured in Lost in Transalation), and then Chion'in, which is a close walk. I would make sure to hit Kinkakuji (Temple of the Golden Pavilion), and Sanjusangendo (Hall of 1001 Kannon).
If you decide to come in the late October (you mention early, I recommend later), you'll be in the Koyo season, or the Leaf-Changing season. As such, do not pass Go, do not collect $200 until you see Tenryu-ji. It is the single loveliest place to witness Koyo that the entire earth may provide. And you can make a full day out of it by going to Katsura Villa in the morning, and sticking around Tenryu-ji through the afternoon and until dusk.

Osaka can be a day trip from Kyoto, meaning you won’t really need to find a place to stay and whatnot. Osaka is definitely my favorite metropolitan city in Japan (it stomps the hell out of Tokyo, if you ask me), but it doesn't house the numerous shrines that Kyoto has, and as such doesn't need to be a landmark in your trip. I suspect you're coming to Japan for the aesthetic nature, rather than the party scene. If this is such, wake up late on day in Kyoto, get over to Osaka, see Umeda (and the Umeda Sky Building), and the Osaka Aquarium. Then, if you want and are feeling energetic, pull an all-nighter and hit up a club in Osaka. If you want a club where you might meet some foreigners, I'd recommend Sam and Dave's #s 2 or 5, both of which can be found a short walk from Yodoyabashi or Umeda. If you want to practice your Japanese (provided you speak any to practice), I personally like the club Za'Zae in Umeda, or Neo in Triangle district.

Then, I would take Bundy's advice: head south. You cannot pass up Miyajima: it is one of Nihon Sankei, or the "Three Beautiful Views of Japan." The floating O-torii is magnificent, and Itsukushima Shrine is badass as well. And though a typhoon in 1997 (if i recall correctly) caused some damage, it didn't level the place. The vast majority of the original structure remains. Miyajima also has one of the three five-story pagodas in Japan (though the name deserts me). And if you have a day to spend, CLIMB MOUNT MISEN. It is the single best thing I did on my trip. The view of the Inland Sea is beyond words.

I, personally, would then continue south and see Fukuoka for a day, and Nagasaki for a day or two. I personally enjoyed Nagasaki's Hewa Kouen, or Peace Park, more than I did Hiroshima. But that may be just me.

I would then fly out of Kansai International Airport in Osaka to save on traveling time and not have to go all the way back to Tokyo.

If you have any other questions, just post 'em. But my greatest piece of advice is to cut short your time in Tokyo and use it to see things that, in my opinion, are more worth the time and money you spent to get here.

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