Japan Accommodation?

I used to leave in Japan and I can say the following

Ryokan....A must experience but is very expensive especially finding the ones that cater to forgeiners. If you do go this route one night remember the shoes never touch the tatami, you are sleeping and eating on the floor, and may have to figure out how to wear a traditional japanese robe.

Love hotels...nice but no in and out privledges. think about the purpose it serves

Capsules....a definite must experience about 3500en and maybe more if it has a onsen (a definite must do-read up on it though before you go)

Hostels...they are nice but we all know hostels are shady anywhere.

BUISNESS HOTELS....(like white hotel or green hotel) this is the way to go about 5000en (~50USD) per night and it is a small room enough for a few pieces of luggage and your tv. and it is all yours and you can come and go as you please and there are no curfews like at some hostels. At the major train stations there should be an information booth, the person there should speak english (99% certainty) and they can direct you with a MAP ( a must have as japan doesn't have street names on most its streets) to the closest, cheapest, most foreigner friendly (Japanese are notorious xenophobs and will discriminate against you because you are not Japanese, dont let that ruin your trip, just be prepared and remember you are not in the US so raising a stink will only get you arrested in Japan) hotel. The business hotels are clean and the front desk may not speak much japanese but they should be able to get you through. Some business hotels even have electronic kiosks with english prompts for checking in and out.

The place I wanted to recommend to you in Tokyo is closed for renovations until the end of spring. That's too bad because it's across the street from Tokyo Station (very handy for setting off for Osaka and Kyoto). The rooms are large and not expensive. However, they recommend

http://www.ryumeikan.co.jp/honten_e.htm

Tokyo Japanese Style Hotel Ryumeikan

They're near Ochanomizu Station which is a JR station. Handy if you're using a JR Rail Pass. It's also three minutes' walk from three subway stations.

I'm sorry, I can't recommend anything first hand in Osaka or Kyoto as I have only stayed with friends there, but you're bound to have a great time in those two very different cities.

You are a couple so don't overlook staying overnight at Love Hotels. If you check in after 22:00 or so you can stay until 09:00 or so for about 8000 yen. You would be getting a bargain on luxury accommodations couples pay much more for during "prime time". Minshuku might be another way to go. At a YA you are not going to get a couple rate-but it's cheap. Capsule hotel don't make all that much sense for the both of you-maybe 3500 each?

I've stayed in the White Hotel in Kyoto and it was pretty nice. It's close to Kyoto station and its about $40 a night (without breakfast). Be warned though, it's hard to find.

Kabuki-cho in Shinjuku, Maruyamacho in Shibuya, and there's one somewhere close to Uguisudani Station near Ueno. Ikebukuro, Roppongi, and Kinshicho may have a couple of interest there also.