I tend to agree. That 2 day/ 1 night special lets you arrange your return any time you want. I'd just stay an extra day in Kyoto and book my own hotel for the second night. Kyoto has far too much to see to cram it all into two partial days. A nice business hotel will only add 6,000 to 9,000 yen to your total. Couple that with a 1-day bus/subway pass and see some of the sights on your own. If you are not sure where to go, the Tourist Information Center on the 9th floor of Kyoto Station has english speaking staff who will give you a tourist map and other information and help you decide. Kyoto is actually one of the easiest places for a first-timer to navigate and enjoy.