Obviously he will go to the wii. This was hinted at almost a year ago that he wanted to develop for wii, and now is his chance.
http://www.nintendowiifanboy.com/2007/08/02/itagakis-kids-want-a-wii-game/
He knows there is little future for the Xbox 360 in Japan. If he wanted to continue on the 360, he would not of resigned.