I agree with Thursdaysd. Japanese style rooms are great for two people sharing a room. The futons are very comfortable, and you have a bit more room since the futons are usually not put down untilitis sleeping time.

Hiroshima ...
We only used twin beds in Japan last month. Most were the very comfortable ( big surprise to our aging bones) futon beds, however our Hiroshima stay might really be of interest to you.
We stayed at JMS Aster Plaza Hiroshima International Youth House . Booked directly through them.
Paid 16,560 yen for 2 nights which is their discounted rate for foreigners on their largest twin with ensuite room.
All linen, towels, soaps, free wifi, etc supplied. Very large room overlooking the river and 10 mins walk from Peace Museum.
More like a 3 star hotel, quiet, very clean, and friendly helpful staff.

Forgot to add, they weren't futon beds