Early September is still hot and humid, but it gets better as the month goes on. Typhoons often hit further south, especially around Okinawa and Shikoku islands, but the further north you go the less you have to worry about the weather. Tohoku and Hokkaido regions rarely see typhoons.
If travelling around Tohoku, you’d be surrounded by nature at all turns, beautiful temples, hiking spots, smaller cities and many traditional towns. Tohoku is generally a rural area and more off the beaten path, so you’d get to know a side of Japan that doesn’t often feature on other tourist’s itineraries. The numerous rice fields are especially beautiful that time of year.
You could combine that with a visit to Hokkaido island, the northernmost tip of the country. It will be the start of autumn up there with autumn leaves starting to appear in many places from mid to late September. September is also a great time to see bears in the wild (safely and from a distance with a professional group).
Near Tokyo there are autumnal grass hills changing colour and a few varieties of red flower fields that make for good day trips. The further south from Tohoku you go, the hotter and more humid it will be.
September is a good time for festivals though, with many towns and cities welcoming the arrival of autumn with folk dances, big events, tea ceremonies and parades. The most important event of September is “tsukimi”, traditional moon-viewing parties, which falls on September 13th next year.