It is a nice time to travel and you have a long time so you can pretty much see whatever you want. I'd start by writing down the places that interest me and then work out an itinerary from there.
For skiing you could consider Hakuba which was open until may last year. You can access from Tokyo, Matsumoto or Nagoya fairly easily.
If you are on a budget you may wish to consider something like the Willer Express bus passes.
If you are happy to allocate the cost of a rail pass in your budget then I'd probably spend the first few days in Tokyo and then activate a 21-day JR Pass (or maybe a 14-day JR Pass), and then spend the last day or two in Tokyo.
I'd try and spend the last few days before Tokyo in Kyoto due to the Cherry blossoms. You may find it easier to stay in Osaka and commute to Kyoto each day.
With the rail pass you can either move around or pick somewhere as a base and do day trips from there.
I'd look through some of the suggested national itineraries on Japan-guide if you need some ideas.
http://www.japan-guide.com/e/e2400.htmlI'd probably at a minimum include Hakuba for your skiing, Matsumoto, Takayama, Shirakawago, Kanazawa, Kyoto, Nara, Osaka, Hiroshima, Miyajima.
I'd consider Fukuoka too, but realistically the world is your oyster, so pick and choose places of interest. I'd just be aware of the cherry blossom timing for Kyoto and Kanazawa at least.
If you are on a tight budget you can consider fewer places but see them in more depth, you can also consider various hostels or even something like couchsurfing if you are trying to keep costs down.
Enjoy your trip!