3 nights.Where to go?

Hello everyone,
Me and my partner are hopefully visiting Japan for the first time in November for 14 nights.So far the itinerary looks as follows:-
5 nights Kyoto.2 nights Hiroshima/Miyajima.2 nights Kanazawa.2 nights Takayama.
Any suggestions on how to spend the remaining 3 nights?Tokyo for all 3 perhaps?Or maybe 1 night in Shirakawa and 2 somewhere else?Any ideas will be much appreciated.Thanks!

For a first visit, Tokyo deserves at least a couple of days.

If you don't mind tighten up the itinerary to visit more places, 1 day each for Hiroshima/Miyajima, Kanazawa and Takayama maybe sufficent. Even Kyoto can be cut back a bit. For the extra days, consider Koya-san, Shirakawa-go, Hakone and Nikko.

The best answer will depend on your interests and how you are travelling (on a JR pass?, arriving/departing at which airport)

But without really knowing what your goals are for Japan, I'm just listing various options on your travel route.

As a daytrip, Himeji is always a good place to see what is probably the best castle in Japan. It's also on the Shinkansen route and is easily accessed from Kyoto (~1 hr)
http://www.japan-guide.com/e/e3500.html

If you like hiking, another day trip or over night stay from Kyoto is the Kiso valley towns of Magome and Tsumago. It's about 2-2.5 hrs from Kyoto by Shinkansen and Ltd express. The towns are preserved to look like old Edo towns and the 3 hr hike between them takes you past a couple of waterfalls and some nice forest scenery.
http://www.japan-guide.com/e/e6075.html

North of Tokyo (2 hrs) is Nikko, which is a major temple complex sitting in a National Park. It could be a nice 2 day trip, one day to see the shrine and temple complexes (which are rather different to those of Kyoto), and one to explore the nearby lake, waterfall, and forest, especially with all the autumn foliage in November.
http://www.japan-guide.com/e/e3800.html

And of course you can easily do 3 days in Tokyo--for me, I had 3 days filled with shopping, wandering the many different neon lit districts and of course lots of eating and drinking.

OK, so lots of rambling from me, but I've only suggested a frraction of the options for those extra days. Just figure out what activities you like and where you'll be with those extra days and you're sure to find a place for it on this site.

I assume you have a JR Pass?
Your plan looks fine: and personally, I'd leave it as it is and spend the last 3 nights in Tokyo:it IS the capital, and a fabulous vibrant contrasting city full of history and modern fun.
The 2 nights you have planned in the 3 places allows a relaxed pace of travel: to my mind there is nothing worse than lugging baggage to a different place each night, quite apart from the time taken actually getting to and from your accommodation every day.
It does depend on your flights though: sounds like you are in and out of Kansai?
If you wanted to skip Tokyo, it could be possible to go south from Hiroshima to Kyushu, and see all that island has to offer. Day trips from Hakata (Fukuoka) as an option: Nagasaki, Imari porcelain areas etc

Thanks to everyone for your replies.
It looks as though those 3 nights will be spent in Tokyo.Just one more question.Should I keep that fifth day in Kyoto and use it as a day trip to Nara,or use it as an overnight stop in Shirakawa instead.
Once again,thanks for all your replies.

Ok everyone,I think I've finally worked out a 14 day itinerary flying into Kansai and leaving from Narita.
Kyoto(4 nights)incl.day trip to Nara.
Miyajima(2nights)incl.day trip to Hiroshima.
Kanazawa(2 nights).
Shirakawa (1 night)
Tsumago(2 nights) incl. day trip to Magome.
Tokyo (via Matsumoto castle)for 3 nights incl. day trip to Nikko.
How does this sound?Hopefully this itinerary could give a nice balance of things to see while not being too rushed.

It's a pity to see Takayama is no longer on the list.