First of all, it depends when do you intend to travel. Autumn extents from early October to early December, so this gives a great range of possibilities...
If you browse a little the guides on this web site, you probably will find lots of ideas for your trip. Here is a small list of places I really like in autumn :
- Towada-ko, a beautiful lake surrounded by forests that turn red in autumn.
- Hachimantai area, with amazing hikes in a very active volcanic activity - great colors in autumn, too
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Tanigawa-dake is a mountain range where you can have great views on the surroundings.
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Oze area is amazing, too - it is the highest march in Japan
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Kami-Kochi area is one of the top place in Japan in autumn, so it can be very crowded, too. Great is you can visit during the week.
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Kyoto, in November, is probably the place in Japan where you will make the best pictures!
Those are only my obvious choices, I think I could find many more attractive destinations to visit at the end of each year... It also depends what are your interests : hiking (a must at that season, onsen (a must, too!!), photography, culture, ...