Tokyo was basically closed when we went, and we still had an amazing time. That's a strong endorsement for visiting Japan. It was the last stop for us on a two-week excursion that began in Hong Kong, and continued through Malaysia and Bangkok. Despite the language barrier (which exists more than you'd think in a global alpha city like Tokyo), Tokyo was the easiest. Maybe it was the cooler temperatures that lowered our stress, or the absence of being pushed in crowded places (crowds were present, but were calm and maintained boundaries), or maybe it was that we took it a little easier being the last leg of the trip. Whatever it was, it was nice.
Back to my first statement: we now know to avoid Tokyo the week of New Year's Day. We knew a few things might be closed, but so much was closed that we were a little disappointed. There was no shortage of things to do, but some places we had looked forward to were shut for the holiday week. Lesson learned. I suppose it's a good reason to go back, which we'd like to do anyway.
As mentioned on my Thailand page, we flew Premium Economy on an ANA red-eye flight from Bangkok. The Narita Express gets you into town, and from there, it's a lot of walking and making use of the extensive and efficient public transportation. Tokyo is no doubt sprawling. On the outbound, we used miles to fly Business Class on Japan Airlines, which was the perfect way to end this trip. For starters, the lounge in Narita is right up there with Cathay Pacific's lounge in Hong Kong. The peace we felt resting in perfectly-shaped chairs, in a cool, quiet, open room, while sipping tea and watching planes land was almost worth the miles alone. Then there's the onboard experience. The seats are incredibly spacious and private, but with the option to converse with your travel partner. (Cathay's seats separate you too much to make that convenient; JAL gives you a motorized privacy wall. And yes, we did have fun with that.) The service, of course, goes without saying.