Typhoon season in Japan late August - early September. Which areas have better weather?

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Rule of thumb: south = bad. If you're on a small island in Okinawa when a big typhoon blows through, you'll indeed be stuck there for a few days because all flights and ferries will halt. But if you're anywhere on the main islands (including places like Kagoshima, which is still on a Shinkansen line and not particularly "remote"), you're likely fine, because you'll get a few days' warning and can get out in time.

Typhoons are also not really a problem for Osaka (sheltered by bay), Kyoto (inland), Tokyo, or any points north of Tokyo -- they're virtually always downgraded to normal storms by the time they make landfall. Likewise, typhoons always hit the Pacific coast, not the Japan Sea side.

FWIW, I lived in Japan for quite a few years and travel there yearly, and early fall is one of my favourite times to travel: not too hot, not too cold, not too many tourists. This also means you can keep your plans flexible and don't need to book far ahead, because it's off season. Only once have I come even close to being inconvenienced by a typhoon, and that was when a post-typhoon landslide closed the road from Atami to Tokyo, trapping a bus full of my colleagues for a few hours. I, however, had snuck off a few hours early and returned by train, which was unaffected.

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Aug 29 to Sept 12, It is HOT, HOT, HOT and HUMID, HUMID, HUMID, with very little wind.

Some non-Japanese welcome typhoons to bring a bit of wind relief.

Typhoon prediction is fairly accurate. You will have a couple of days of notice if a typhoon is expected to hit.
http://www.jma.go.jp/en/typh/typh5.html

You heard correct about jellyfish. Go to Japan Inland Sea.
A favorite is Shiraishi Island, Amy Chavez "Cow Lady" will take care of you.
http://www.moooobar.com/
dailymoooo.blogspot.jp

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