Rakuten and Jaran in Japanese can really difficult for a few general and a few Japan only issues
First off is once you make a booking in a hotel they automatically sign you up for a ton of mailing lists unless you remember to uncheck them.
Some hotels required you to write something into the comments like if you need to use the parking lot or not. Sometimes they require a comment but have no question to be answered so you fill in with the obligatory "yoroshiku onegaishimasu "
Last big issue is the booking "plans" which are a common thing on Japanese sites. Do you want a room smoking, semidouble, with breakfast and a prepaid cash card for the conbini next door that costs 20 bucks more? For a leasure traveler it makes no sense but for a business traveler on an expense account it does. Having to sort through the options can be tough if your not a native speaker and/or have travel experience .
Also the English sites sometimes don't offer the cheapest rooms. Sometimes for the best! Haha
Good luck with your research.