Cost - $75-$150
Location - short walk to a JR Shinkansen station (bullet trains that we will have almost unlimited access to with our Japan Rail Passes)
Bed size - at least an American double - especially when we realized the common "small double" is just a little larger than a twin size bed here!
Cancellation policy - since we booked our hotels before our plane tickets, we wanted to make sure any reservation we made was 100% refundable (most of the ones we looked at were - we used Orbitz and Booking.com)
Once we found those things, we read reviews on TripAdvisor. My favorite are the very angry, 1 star reviews because "the TV was in Japanese!" and "the room was so tiny!" (always left by Americans - often with the next review being from a non-American: "the room was very spacious!") We get that things in Japan are much more compact than we are accustomed to - and in Japanese...since we are going to be in Japan...(I think some people on TripAdvisor must not be able to grasp that). It was useful to find out how much English the staff seems to know, the quality of the Internet, and what "perks" are included (pretty much breakfast and toiletries at our price-point).
I think the hotels we settled on all look pretty decent:
Tokyo: Best Western Shinjuku Astina Hotel Tokyo
We figured we'll be pretty overwhelmed by the time we get to our first hotel so a Best Western seemed like a good choice since the familiar brand feels a little more like "home." We got a standard double room with a buffet breakfast on Orbitz for $125/night.
Osaka/Kyoto: Shin Osaka Station Hotel
Hotel rooms in Kyoto were hard to find - and expensive when we did - so we decided to use Osaka as our base for exploring the area. The hotel is very close to the Shin-Osaka Shinkansen Station where we can take a JR train to Kyoto in 15-30 min (much shorter than our daily commutes to work!) Our room is an economy double from Booking.com for about $106/night.
Hiroshima: Sheraton Hiroshima Hotel
We plan to spend a couple days visiting Hiroshima and Miyajima so we'll spend one night here - and in a deluxe king room (John was pretty excited about that part!) It was our most expensive room (the king sized bed is a bit of a splurge, but I think we'll deserve it by then) at around $150/night - we found it on Orbitz.
Tokyo: Mitsui Garden Hotel Ueno
We'll head back to Tokyo for the last couple days to stay in the Ueno/Akihabara/Asakusa area. Our double room here was about $135/night on Booking.com.
We are also considering a side trip to Kanazawa - if we decide to do that, we have a room booked at the Garden Hotel Kanazawa. Our double room was about $100/night on Booking.com.
おやすみなさい (Oyasuminasai) and good night!