If you want to see both Kyoto and Hiroshima, I'd highly recommend sone of the packages that JTB has. The self guided tours, which include transportation and hotel are very good deals. This one sounds like it would probably be just right for you.
http://act.jtb.co.jp/itdt/scripts/su...gp=Y&t_no=C260
Includes bullet train tickets for Tokyo-Kyoto, Kyoto-Hiroshima, and Hiroshima-Tokyo as well as one night hotel in Kyoto and one night in Hiroshima.
I had some friends over to visit me in February and we booked this package and went down to both Kyoto and Hiroshima with them. It worked out pretty well, we got to see plenty in both Kyoto and Hiroshima.
Editing this to add:
One thing I forgot to mention, was that for this particular tour, the web form to book it doesn't work right for Tokyo departures - it only lists Nagoya as a departure option - they haven't fixed this on their website. As a result, I had to book the tour by phone. It appear that JTB has a fair number of offices in the US that you could book it, so you wouldn't need to make a call to Japan to book it.
http://www.jtb.co.jp/sunrisetour/