I made reservation through Agoda in Kyoto. Here is what I learned:
1. It is impossible to find out ahead of time the room size (not posted anywhere w. the rooms) or the difference between same type of rooms in the "main building" or "south", on the "standard floor" or "premium floor". I called them. After an 1 hour wait, the support staff put me on hold for another 15 min to check w. the hotel, then came back pro promise to call me back w. an answer. they never did.
2. The room/night cost is somewhat misleading as it doesn't show up-front the HUGE service fees. and taxes, much bigger than on any other site for the same room type, same hotel.
3. While info is posted about the date until cancellation is free, there is no info prior to an actual reservation about the penalty for cancelling after that date. Only when I got the confirmation, I noticed that if a cancellation is made within 10 days of the check-in date, there is NO refund. This has big implications to the travel policy I bought.
You might want to keep this in mind before you decide to use Agoda.