Hi,
I think everywhere will be busy for O-bon ( お盆 )
Kyoto, you can visit Kinkakuji, Ginkakuji, Kiyomizudera, Sanjuusangendou Hall.
Fushimi Inari, Nijo Castle, plus other temples and shrines, and a little way out from the centre, Arashiyama and Oohara, are interesting.
There is also covered market area, perhaps not so far from Gion Corner, with many varieties of goods!
If you can, visit some Izakaya as well as other styles of restaurant, such as Kaitenzushi.
Tokyo is ok, Yokohama had an interesting Chinatown ( Yes, I know a strange suggestion when you are going to Japan! ), Hakone Onsen is not so far from Tokyo and an overnight stay in a Ryokan is excellent, I feel.
I like Shinjuku, but some may feel it is dangerous at times. I think not! I just use my common sense! Tokyo also has Tokyo Tower, Odaiba, Asakusa , Ginza and other interesting places.
Most of my friends do not bother with Akihabara so much, because they feel they can get just as good bargains in other electrical stores.
Give a big smile when your finger print is taken! The person in front of me didn't and he complained !
Hope you have a great time !!
Ofiaich