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It isn’t particularly glamorous but Choice Hotels has lots of options in Tokyo and it is only 8,000 points a night.
I just booked 6 nights for only 48,000 Membership Rewards points!!
The rooms are basically like Holiday Inn and include breakfast but it is super cheap and there are lots of options around town if you want a particular location.
Plus as I said earlier, the points can transfer from Membership Rewards.