welcome to Tokyo(I don't have to be nice to my own city)
things you may not like (compared with HK):
1) clerks at government agencies don't speak English. Some downtown Tokyo city halls have English speaking volunteers, though more of a gesture. the efficiency also seems to be worse than that of HK. many things are still paper based.
2) air conditioning in the subway system is not as strong as that of HK in summer times. seats are padded, heated in winter times so kind of nice, though sometimes it smells of pee inside the trains
3) largely still a cash society, though def changing. you may run into supermarkets that only accept cash every now and then.
4) plane tickets flying out of Tokyo are more expensive, for trips to Europe or the states etc.
5) generally out of pocket co-pay of 30% of your medical bill (with universal health care)
6) utilities are more expensive
7) vegetables and fruits are more expensive
8) movie tickets are more expensive, it takes forever for Hollywood movies to be released in Japan, 3-6months at least.