Well, backtracking is usually inefficient and can waste time/money, but that is not your only consideration. I take it that your itinerary above is still a rough draft and needs to be worked out a lot more. Two weeks in Tokyo? Unless you have some specific ideas or events planned, I'd say 3-4 day are enough. There are many good day trips in the area - and you can certainly expand your trip in many ways if you want to allocate the time and money for it. A Tokyo Wide Pass (or 2) could really help you here.
http://www.japan-guide.com/e/e2361_06.htmlGiven the long length of your enviable trip, you travel pace is not going to be very fast or very far - so a series of regional rail passes would likely serve you better than the full JR Pass.
http://www.japan-guide.com/e/e2357.htmlEvery place has something to see, but since you are already seeing Tokyo, you can largely skip Osaka during the day. With that time you could see more of Kyoto, like Miyama, and Amanohashidate, plus there is nearby Himeji with Japan's finest castle, and you could also do a day trip (and preferably overnight) to Hiroshima and Miyajima.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-iCNZ6AdsKGUB-HPKNxP1...With the time you have, skipping Kanazawa would be a terrible shame.
Also not sure why you're going to Niigata (Sado is great, and if you drive there are of course some nice places) and 3days for Sendai, unless you're branching out or going to the rest of Tohoku too.
Okinawa and Hokkaido are also possibilities, and it's very cheap to fly there on Jet Star, Peach, and Vanilla Air.
You could certainly put more time into the Chugoku area - in addition to Okayama City, Hiroshima, Naoshima, you could see Onomichi, Kurashiki, and Iwakuni. Even venture into Shikoku a bit and see Takamatsu, and Kotohira.