I like Japan a lot, everything not on this list is probably better in Japan, but these are the few sucky things I've found here
  1. Money/banks
    Everything is cash only. Banks are shut on weekends and after 5 pm. All ATMs are inside buildings. Banks take 2 weeks to process any forms. Everything is done on paper/hand written. Prices often end in something-and-1 yen, giving you 9yen of pointless change
  2. Phone contracts
    2 year contracts, and ridiculously high prices. Plus it literally takes hours to fill out all the forms when you sign up
  3. Business culture
    Staying late for no reason other than to impress your boss. Literally people here sit at their desk staring at a blank screen in order to 'look busy' and stay in the office longer. People never take sick days, and rarely use vacation days. If you do something wrong, they act as though everything is fine, but complain to your boss behind your back
  4. Students
    Teaching English conversation is a struggle because students are either shy, don't care, or just suck at English. All 3 result in nobody wanting to talk in class. It is almost physically painful watching them sometimes
  5. Technology
    You wouldn't expect this from Japan, and they have some really advanced tech available. But in reality, companies/a lot of people are still using technology that was outdated a decade ago. Try musing Windows xp or a fax machine... it's insane