Both have their positives and negatives.
As with MM and Damicci I would prefer to be just considered a citizen of the world and be able to live without hassle anywhere I chose. However, if I were living in Japan I would still rather be American as then I would still have the "gaijin card" to play, so to speak, in that I would not be expected to conform to Japanese customs and standards. In other words, I could be me with a free pass while living in a country I greatly enjoy.
Even if I were to change my nationality to Japanese (and I may) after I move back, most Japanese would never know it and I could still get by with my gaijin pass. I think it would be alot harder for a Japanese-American to get the free pass as, just by his/her looks, they would be deemed Japanese and expected to conform. It would be alot harder to live in Japan as a Japanese-American I think.
Based on the loss of freedoms in the USA today, I would have to say that it wouldn't matter one way or another as I felt quite free while living in Japan even though their legal system is quite different from the US'. I would be more afraid of getting arrested in the US today than I would in Japan. I just don't know which way I would vote right now, so I have not voted. Interesting thread btw.