Hi ChloeW,
Autumn in Japan is a beautiful time to have a honeymoon. The nature is beautiful and its not too hot and humid like the summer and definitely not cold like January of February.
I would say a beautiful part of Japan during this time is Hakone and Kyoto. Maybe stay a day or two at a ryokan instead of a hotel. Go to an onsen, too. Tokyo is always a place you should visit, a lot of restaurants and cafes open their terraces and provide blankets and heaters if it gets a bit chilly during the cooler months.
Also, to be honest, I would say just do research on blogs, reviews, etc on Japan and do your own tour without a tour company. English is not usually a problem- signs, directions, menus, etc can be found in English, Chinese, and Korean and if anything, people are usually more than willing to help!
Sue
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