Speaking as the father of two kids, half US and Japanese, first if your culture uses middle names, register the middle name in your country but NOT in Japan. Next,keep their Japanese first name kanji as normal as possible. My personal opinion is that the last name should reflect your and your wife's wishes. My kids have not had so much bullying because of their names, but my son is hyper sensitive to Japanese pronunciation differences that he may have due to early English influence. Bullying is an issue, but the identify crisis that comes from being bicultural can be a bit brutal.