I specifically ensure that there is no middle name/initial on any of my bookings. Because my IDs (drivers license and passport) have my middle name but in one instance it's hyphenated and in another it's not, I've decided it's more trouble than it's worth. No one has ever given me a hard time that I have a middle name on my ID but not on my ticket.
The goofy thing that JAL does is it compresses the name on the reservation with "MR" or "MRS" and then you sometimes have issues looking up your reservation because there's something added to the end of your name