I'm pretty partial to all the adorable mascots in Japan. Almost everything has a cartoon mascot--malls, foods, banks, even jello cups!
I also absolutely love conbini, the convenience stores everywhere in Japan. They aren't like western convenience stores. They have delicious bentos, juices and teas, cool anime collectables...just about anything.
And my other favorite thing is how polite Japan is. It's very much a culture of putting others first and thinking of their needs, which results in a really safe, really clean, and really pleasant environment.
That said, Japan has its pros and cons like any country, but these are some of the things I really enjoy when I'm there. :)