Best way to get to our destination

We will be traveling to Japan from October 10 to 16th. We plan to travel to following places
10/10 arrived Tokyo
10/11- go to Hakone
10/12 Tokyo
10/13 Tokyo to Kyoto, then transfer to go to Nara, then to Osaka
10/14 Osaka to Kyoto, then head to Nagoya
10/15 Nagoya then back to Tokyo
10/16 depart Tokyo

Where can we save best? Buy the National JR Pass, Regional pass or individual passes? Thank you