Awesome, you'll love Japan!
Hokkaido is technically doable in your time frame, but I wouldn't recommend it - you're going to spend 2 of your 3 days just getting there and back. Not saying Hokkaido isn't worth going (actually going there in February myself,) but with your tight schedule I think you should focus on the many great places closer by.
Kyoto on the other hand, I would definitely recommend. It's less than 3 hours from Tokyo by shinkansen. There are some really spectacular temples and shrines. I've been there many times but never in winter; I bet it would look fantastic if you're lucky enough to have snow coverage (I've got my fingers crossed for February.)
If you want to check out a castle, go to Matsumoto Castle, near Nagano. Most castles in Japan are post-war concrete reconstructions - still pretty cool, but not quite the same thing. Matsumoto-jo on the other hand is one of the few remaining originals and considered one of the most beautiful.
Nara and its Great Buddha is within spitting distance of Kyoto, though Kyoto might give you your fill of temples.
Nikko is a great day trip north of Tokyo. It holds the mausoleum of Tokugawa Ieyasu, the founder of the 300 year long Tokugawa Shogunate and the most powerful man in Japan's history. It's ridiculously over the top.
Get a JR Pass. If you're doing any traveling it's an incredible deal.
Around Tokyo, I recommend the Tokyo International Forum, something you won't find highlighted in most guidebooks but is photography candy. Go at night.
I also recommend riding the Yurikamome line - it's a driverless elevated monorail, which means you can sit up front and shoot directly out the front windshield, which gives you a really unique view of the city. Also better at night, though since they shut down all the nuclear plants there aren't nearly as many lights on in the office buildings (great for conservation, not so great for photography.) The Yurikamome takes you across Tokyo Bay to Odaiba, which was mostly developed in the last 20 years and looks like The City From The Future (by which I mean big buildings surrounded by lots of parks and open areas - almost no low rise sprawl at all.) There's also a life-sized Gundam there
I would say check out GCANS, the Tokyo municipal flood control system which has incredible mega-architecture, but they require you to have someone who can speak Japanese with you so that might not be an option.
Go to Tsukiji, the huge wholesale fish market. Take advantage of your jetlag at the beginning of your trip and go at 4am to catch the auctions.