OK, I'm going out on a limb here, total controversy - if you are planning a trip to Japan for the first time, unless you have a particular reason to go there, I'd say skip Tokyo!
Yes, you are reading that right.
Of course, if the most compelling reason for your visit is to do something you can only do in Tokyo, like go to the one shop in the world that sells the limited edition vintage Gundam figurines or shop a boutique in 109 that doesn't have a branch elsewhere, then you are going to do Tokyo, obvs.
If you just want a general taste of Japanese culture but you won't feel like you are actually in Japan unless you stand in the middle of the Shibuya scramble, I'd suggest basing yourself in the Kansai region and doing a day trip to Tokyo.
Otherwise, cross it off your list.
The Kansai region has everything you need - the temples, gardens and geisha of Kyoto, the awesome guadiness of Osaka, side trips to places like Nara and Himeji within easy reach. Plus it's cheaper.
Note: that's assuming you can get a flight into Kansai airport for the same price as Tokyo. You can from Australia, not sure about from other places.
Where to stay:
I don't want to go too much into accommodation. If you don't know about couch surfers or Hostelworld plus the rock bottom options of capsule hotels (which never actually seem that cheap to me) and internet cafes, you can easily google them. Just remember that if you do the capsule hotel/internet cafe thing, as well as disturbed sleep, you'd have to either carry your stuff or get a coin locker during the day.
One thing I do like about the Kansai region is that there is a wealth (my posh way of saying shitloads) of cheap backpackers around the Nishinari area of Osaka. You can get your own room for around $20 a night.
Anyway, I stayed at the Hotel Taiyo but I'd say any of the places in the area would be about the same. The Hotel Chuo across the road looked a bit more upmarket. Chuo has deals for longer stays on their website but you could probably get the same at any of the hotels in the area if you asked.
The hotels have baths so you can check the sento experience off your list without leaving your hotel. the bath is only available for certain hours at night.
It's very close to the Dotonburi area if you want to go out drinking - a couple of subway stops and you could probably walk it if you get drunk and miss the last train (if you have a sense of direction).
The area around the Nishinari is pretty awesome too. When I booked to stay there, my Japanese housemate warned me it was a bit rough but really it isn't. There are homeless people and you might get asked for money but it's nothing like you'd get in Melbourne or probably most Western cities (ie. you don't abused if you don't give money).
|Cafe near the hotel. So retro they still have a functioning rotary dial phone. You can get a breakfast deal with coffee and boiled egg and toast.|
Apparently, after being run down for many years, the area has become a popular dating spot for teenagers. Not that that means much, the Parasite Museum in Meguro is also a popular dating spot.
|Osaka is awesome|
You could easily spend 2-3 days checking out Osaka and maybe half a day in Kyoto. OK, most people would say the opposite but I find Kyoto really boring (and I've never been able to find coffee shops there). To give you an idea of distance, it'd take you about 30 minutes to get from Osaka to Kyoto so it's pretty easy to explore both cities.
|Kyoto - pretty but boring in my opinion|
But wait, there's more.
Grab yourself a Kansai area pass and you can plan day trips to Nara, Kobe, Himeji and more. You could get one to cover you from the airport as well but I'd get this deal to cover airport transfer and few days of travel around Osaka and Kyoto (the Kansai pass is only valid for JR trains and there seems to be a lot of subway travel around Osaka).
To be honest, I've never been to Nara and only been through Kobe and Himeji on the train so I can't really tell you much about them but they seem good places to visit.
For stays of over a week:
I'd get me a me a Sanyo Area pass and head to places like Hiroshima, even down to Fukuoka for some tonkotsu ramen. To be honest, I didn't find Fukuoka that interesting except for the ramen but you could pretty much catch the shinkansen, have your bowl of ramen - in one of the yatai (food stalls) then leave town.
Note: I've been told that Fukuoka has the prettiest girls in Japan but I'm no judge of that kind of thing. Btw I'd say Osaka has the best looking guys.
|How do they take the tourist pics without the hordes of people?|
Even longer trip:
What I'd do is, after exploring the delights of Osaka, book a cheap flight from Osaka to Kagoshima on Peach or one of the other budget airlines (should be around $50) and, after exploring Kagoshima for a few days, use my Sanyo-Shikoku-All Kyushu pass to get back (including taking in all the places listed in the section above).
I actually wish I'd known about this before I did my "I heart Sakamoto Ryoma" tour last year because it covers everywhere I wanted to go.
Note: all these passes only over the bottom half of Japan. If you want to include Tokyo you need the full JR Pass which is much more $$$ or you can save money and catch a night bus. I think the reason I didn't use this pass last year was because I needed to get to and from Tokyo.
For my five days travel, I'd skip Nagasaki unless I had some strong reason for going (ie. Sakamoto Ryoma) - it's one of the most beautiful cities I've been to but it's a pain in the arse to get to especially on a 5 day pass since it's off the shinkansen line.
I'd definitely go to Shikoku. Even if you don't love Sakamoto Ryoma, Kochi is worth a visit for the katsuo. This local variety of seared tuna is pretty much the best thing I've ever put in my mouth.
|Katsuo - far more delicious than it looks in my crappy picture|
I don't know much about the rest of Shikoku but I'm thinking of actually getting this pass and doing some more exploring next time I go. I know there are some pretty awesome bushwalks around the area (I'm not sure if I know this from real life or reading Kafka on the Shore though!)
I also don't know if you can buy more than one pass. The pass covers 5 days but, if you wanted to really explore, you could use one then base yourself somewhere then use the other 5 day pass.
The cheapest option
If you have a lot of time and like slow travel, then I recommend the Seishun Juuhachi ticket. You need to travel at the right time of year (usually Japanese school holiday times) but for around $100 you get 5 days travel on local trains. I wrote a post about it a few years ago so check that out. Note: the post has no photos in it because I went over my photo limit on blogger and deleted a lot of old photos. You can buy multiples of this pass and even share it with other people.
You might need rudimentary Japanese to use this pass especially if you plan to go off the main lines. Some of the smaller stations don't have English or English speaking stuff. Knowing the basics like toire wa doko desu ka comes in handy!
Okay, that's my ideas of Japan travel itineraries. I wrote this off the top of my head so might have missed stuff out. If you have any questions, ask away. If you live in the Kansai area and can think of any awesome stuff I missed out, let me know (or tell me I'm full of shit and reasons why you should go to Tokyo).
I might post up a Tokyo itinerary later (since I have one in word that I did for my sister of alternative plans).