Originally Posted by
pogonation
If possible I would like to climb a small mountain, see some waterfalls, fishing villages etc and maybe end the day at a small, interesting town/city.
What exactly do you want to do?
If you can come up with something more specific people can give you some advice. I (and several others here) live near Kyoto and we can tell you about mountain climbing, waterfalls, and some coastal places.
Also, don't bother renting a car. The rate for renting it is expensive, tolls are expensive, parking it is expensive, and gas is expensive. Unless you have money to blow and are willing to sit in traffic a lot, just don't bother with it.