If you intend to travel to those places and back to Osaka, then the Kansai Thru pass is probably not worth it. The tickets from Osaka to/from Kyoto, Kobe and Nara is quite cheap (about 300 to 600 yen one way).
However if you intend to move around when you are there, then it may be ok. For example;
- Osaka to Kobe plus visit to Himeji, Arima Onsen, Mount Rokko, Akashi Kaikyo Bridge etc.
- Osaka to Nara plus visit to Fushimi Inari Shrine, which is actually in Southern Kyoto.
You need to do your sums.
Look at this link for examples;
Japan Rail Pass and rail travel in Japan complete guide – JPRail.com » Blog Archive » Kansai Thru Pass sample itineraries
Subway in Kyoto is not very useful. You may be better off using their buses. A day bus pass worth 500 yen.