Depending on how much you want to do, you can reasonably tick off the major points in both Kyoto and Nara in a day. We managed to do the Arashiyama bamboo forest, Tenryu-Ji Temple and flower garden, Fushimi Inari Taisha Shrine (Thousand Torii Gates), and then detoured to Nara to visit the Deer Park all in the same day.
While in Osaka, we enjoyed the Tempozan Aquarium and Wheel. Universal's express pass was essential. Staying on property at universal also means you get the inside scoop on what time the park will open the next day (the park has publicly advertised opening times, however gates open well in advance of those times and the hotels generally know what time it is planned to be, and if you haven't paid the premium prices to guarantee entry to Nintendo you'll need to be first in the park to guarantee you get yourself a timeslot.
I'd encourage a visit to Hiroshima Peace Park. Miyajima was also on our list for a day-trip but other events changed our plans and we didn't get to go.