It would be protocol if he wanted to admit that America’s leader was inferior to Japan’s royal couple:

A senior administration official said President Barack Obama was simply observing protocol when he bowed to Japanese Emperor Akihito and Empress Michiko upon arriving at the Imperial Palace in Tokyo on Saturday.

Here are examples of how other world leaders greet the emperor of Japan (here’s a link to a video of 46 world leaders not bowing). I think it’s time Obama had world leader remedial training so that he doesn’t keep making this kind of embarrassing gaffe (one Clinton almost made in 1994 and was rebuked by the NY Times for doing so — here’s what the Times is saying about Obama’s full out bow)Notice how the royal couple respond to his gesture: