Use Kyoto as the base, can do:
Temples in Kyoto area, Kyoto Imperial Palace (pre-booking required), Kiyomizu-dera, Kinkaku-ji (go on a calm day), Ryōan-ji area with multiple temples.
One day trip to:
Hiroshima, Atomic Bombing. Get off the train, take a bus.
Itsukushima Shrine, better go during high tide. Oysters are very famous on this island Miyajima.
https://en.wikipedia.org/wiki/Itsukushima_Shrine
Okayama Korakuen if spring time, https://en.wikipedia.org/wiki/K%C5%8Draku-en
Day trip to Osaka and/or Kobe;
Day trip to Nara, which is famous for Todai-ji; Hōryū-ji; Kasuga-taisha; and lots of deer
Day trip to Nagoya, - I've never been though.
Stayed at Royal Park Hotel The Kyoto, very close to shopping arcades, including Nishiki Market. Food stalls close at 6pm.