Hi!
I meant that Kanazawa just has better connections to Kyoto and Tokyo than Takayama does, and it is a shorter trip from either. I guess I should also throw out there that depending on time of year certain options make more sense than others. I've been traveling in June/July because that is when my daughter has off from school. All of these areas are really different in Winter. My first trip to Takayama was in February.
With a trip to Miyajima and Nikko then, yes, a pass is probably worth it.
If you want to leave early enough you could do Kyoto to Kanazawa and see the garden. If you're not also going to Ritsurin you are unlikely to be disappointed like my daughter. You could then do Shirakawa Go or just take the bus direct to Takayama, since again the Hidas from Toyama to Takayama are only so frequent.
But if you can time for one, it is faster, you'll just skip Shirakawa Go. It's a bit easier to time from Kanazawa because there are Tsurugis, the shinkansen shuttle that only runs between Toyama and Kanazawa. (So there are more frequent connections between the two than Toyama to Nagano and Tokyo.) Keep the 2 nights in Takayama and then bus it to Matsumoto, I think that bus trip is lovely and I like Matsumoto. It's about 150 minutes from Shinjuku Station or 170 minutes to Tokyo Station by way of Nagano. This route will cost more, since you take the shinkansen from Nagano. I would not do this unless you want to go to Zenkoji and you have a rail pass.
I'm pretty sure the 3 Star route ticket would be valid from Kanazawa to Matsumoto (but you can't use the cheaper bus fare to Shinjuku when coming from Tokyo.
http://www.alpico.co.jp/access/ticket/pdf/panf701[1].pdf
So for 5500 yen it would include a lot of your buses. (Kanazawa to Shirakawa Go to Takayama to Matsumoto, if you trip is in the Summer you might want to stop in Hirayu and either check out Kamikochi or the Okuhida region, both would cost additional but not so much.)
Matsumoto should be much cheaper than Tokyo for lodging unless you are staying at a fancier ryokan and then meals are likely to be included. We enjoyed the Castle, the small art museum, and the unique water fountains through out town.
My daughter would have loved to have spent more time in Hida no Sato village in Takayama, but I was afraid I lost something in my hotel and I didn't know the 12:30 train didn't go to Toyama because I stupidly failed to check Hyperdia ahead of time.
Enjoy!
