I have been visiting Japan in Feb every year in the last few years and it had always been nice experiences. This year I spent a few days in Mito and two years ago a few days on Noto Hanto at Wakura Onsen.

As mentioned by other posters, winter is less crowded, air is more crisp, and gardens are less dusty. My first trip to Japan as a teenager was in Jan and that's how I remembered this country.

The only problem with combining Phuket and winter Japan is clothing. You will need to lug around warm weather clothes and cold weather clothes (shoes too). I did the same a few years ago combining Nanjing and Singapore on the same trip and had a heavy coat in Singapore.