I like to think that that saber colors are like belt colors in martial arts. Blue is for affirmed Jedi knights. Green are for Masters. Purple is for Grand Sword Masters. In keeping with that, I'd figure Obi-Wan never graduated to Green cause of sentimental feelings and perhaps a sense of personal failure, believing that he wasn't worthy to sport a green blase. Since Yoda is apparently a better swordsman then Windu I'd think that Yoda's ego wasn't at stake and simply wanted to stay with traditional green.