JRパス

hmm... Toughie. I personally think Tokyo is a fairly easy place to get over jetlag, with it's 24/7 bars and convenience everywhere. It's also more international than other Japanese cities, so there's a bit less of a culture shock when you land - more english signage and so on.

That said... I do think that it's a shame to fly in and out of Tokyo. Much better to fly out of another Japanese city, like Kansai International (Osaka), or Fukuoka. I think the air ticket type is called 'open jaw', and it lets you get another good 2 days of sightseeing into a 1 day trip (rather than worrying about getting back up to Tokyo)

My ideal 7 day trip would be to land in Tokyo, and then gradually work my way down to Kansai International. you can pack a lot into the things in-between, including Kyoto, Nara, Koya san, the Mt Fuji area and Yokohama, not to mention Osaka itself. If you were feeling energetic, you could even do a quick 1 day trip down to Hiroshima/Miyajima, which is a 'must visit' for any holiday in Japan.