Hi,
Unfortunately a full JR Pass would not save you any money for your plans. Something like a JR Kansai Area Pass could be used to save you some money getting from the airport into Kyoto. But if you are only staying in Kyoto, or just going from Kyoto to Osaka, then buying regular fare tickets would be the best bet after that. There is no pass that covers all the trains, subways and buses. There is the Osaka Amazing Pass, which covers transport only within Osaka, plus a Kyoto bus pass and Kyoto bus/subway pass.
You could use the JR Kansai Area Pass also if you wanted to go see Himeji castle, which is Japan's finest. Visiting Nara for at least half a day would be an excellent side trip as well.
In Kyoto you could spend weeks there and not see everything. The three best sights though are the Kinkakuji Temple, Kiyomizudera Temple, and Fushimi Inari Shrine. Fushimi is the most time consuming; you could spend a couple of hours to over half a day if you want to romp over all the trails.
And the Otagi Nenbutsuji is one of the most humorous and whimsical places you could visit in Japan - well worth visiting.
At night Osaka comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg are beautiful.
Best of luck.