Well the last few flights I have taken to Japan (including JL3) were red eye flights arriving in the early morning. My reasons include:

• I don't like waking up at 5-6am for morning flights if I don't need to do so. I don't sleep well the night before due to me being concerned I'll miss my flight. Red eye flight means a relaxed trip to the airport, dinner at the lounge, quick nap on the plane, full day in Tokyo/easy connection to a smaller city.
• Arriving in the early morning means I'll get to my hotel by 8/9am. I always drop my bag off, go to a fish market for breakfast, and then continue having a full day of fun before checking into my hotel in the afternoon. The afternoon flights arrive to late for any sort of adventure so it's a waste of a hotel night like mentioned previously.