get a day bus pass (for 500en) from the bus place infront of kyoto station. then you can travel all over kyoto all day long as much as you want (the bus fare are pretty expensive in kyoto, over 200 en i believe). As far as what to stop at, theres a looooooooot to see in kyoto. Some of my favorites were : kyomizudera, gion, nijoujou, kinkakuji. But really, theres soo much to see, you can even do it on a whim the day you arrive because they give you a map with your day pass with all the sites. I suggest spending more time in Kyoto because it has a lot more to see than Osaka and I didn't get to see as much as I liked to in 2 and 1/2 days, I'm afraid 1/2 day is really not much. I probably spent ~2hrs per temple/castle.
For osaka area, Namba is really cool for food/shopping/people watching...amazingly huuuuuuuge shopping place. And the crab & glico man are there (famous in japan)
