As others have said, sounds like a good time to go for you (you'll find it much easier/more pleasurable to cram in activities than in the summer months).

Only downside I've found (besides the sparks, husband has very dry skin) is the possibility of serious snow and ice in the mountainous areas close to the cities. One cold day on January 1st not so very long ago we passed hikers dressed in what seemed to be excessive winter gear as we climbed up Mt Takao (an area just an hour away from Shinjuku by the slow local train). As we reached the peak, snow descended in abundance and the descent - an easy enough walk which can usually be done even with an urban stroller - was covered in ice and snow and became treacherous.

It could be that there won't be any snow before 2014, but it does happen frequently enough to consider it. Personally, and just from experience rather than from official figures, my own winter plans for Tokyo assume a 33% chance of snow (50% if going in January, which is when I'll be there next).

In summary; if you have plans on going anywhere rustic towards the end off the year think about fitting these plans in earlier rather than later so that snow can't scupper them, and if you do go anywhere, pay attention to what the locals are wearing. Our thought was that the 'excessively prepared' hikers had been given new winter climbing gear as holiday gifts and wanted to try them out. We were very, very wrong. I still to this day do not know how we managed to get down without a broken bone.