For the trip you describe, you can save 7,300Y (about $94) by buying the Tokyo-Kyoto Open Ticket Package -- 21,000Y for that package, compared to 28,300 for the JR pass. Plus, you can use the faster Nozomi trains, but you will travel in the unreserved rather than reserved cars.

True, you'd lose 1 NEx trip, but you can pretty much make up the difference with a r/t NEx/Suica package.

Info: http://www.japanican.com/tours/tourd...mm%2fdd%2fyyyy