Facebook thrives in much of the western world because it's key feature is over-simplicity. Computer illiterate people feel well at home using facebook.
In a country with a high number of early adopters, they're likely more interested in useful apps over simple apps.
my wife is from tokyo and hasn't been in the US for long. she still doesn't consider this her home, and we live in tokyo for 3 months of the year.
anyway, i mention this because i think she's a fairly good representative of the upper-middle class segment in japan, as are her friends. they have almost no interest in facebook. part of that is due to the fact the japanese have ameba.jp and mixi, which have been around for a while and seem to be the social networking sites of choice in japan.
also, when i've asked my wife why she dislikes facebook so much, it usually comes down to privacy concerns. she's got her account locked down, but she's annoyed she even has to do this (and continually check it to make sure things haven't changed). she also doesn't like having to grant applications the ability to access her account in order to use them.
I was under the impression it had more to do with Facebook's policy of requiring real names. Most Japanese users do not use their real identities online.
In a country with a high number of early adopters, they're likely more interested in useful apps over simple apps.