The bow is this simple: It's the customary greeting in Japan, and it's an act of respect. Now, conservatives are saying that he shouldn't bow because it means that he is saying America is inferior to Japan, and that is not true. A bow, as I said, is only a greeting and way of showing respect in Japanese culture, in doing so Obama does not convey that America is inferior, he conveys that he and America respects Japan and the Emperor. Obama is not the first president to bow to a foreign leader either, both Nixon and Eisenhower (republicans) bowed to foreign leaders, so this isn't anything new. And who can forget George W. Bush holding hands and kissing the prince of Saudi Arabia.
Some conservatives in this country have gone nuts because when Obama is on foreign soil, and as a general policy, he respects the country and it's culture, and the conservatives feel that instead of being the kid on the schoolyard that likes to be nice and help out the other kids and the one that everyone likes the U.S. should be the one running around stealing kids lunch money and shoving their faces in the mud. I for one like it that my president respects other cultures and nations as well as their leaders, as that is how I am and how I would conduct myself, and I for one like it that my president is reversing the global PR damage that was caused by the Bush administration and their polices that made the rest of the world see us as unenlightened disrespectful war-mongering bullies.
This really isn't an issue if you ask me. I doubt the Japanese people made much of the emperor shaking hands with Obama.