The article is not saying GNOME 3/Unity is similar to Win95, it's saying that Steve Ballmer believed that GNOME 2 and KDE 3 (shipped by Red Hat, Ubuntu, SuSE at

The article is not saying GNOME 3/Unity is similar to Win95, it's saying that Steve Ballmer believed that GNOME 2 and KDE 3 (shipped by Red Hat, Ubuntu, SuSE at the time) were too similar to Win95-Win8, which Microsoft owned patents on. And therefore, because of rumblings from within Microsoft in 2006-2007, GNOME had to change as soon as possible, and KDE was fine staying the same because SuSE had been semi-blessed by Microsoft. (The premise of the article is factually wrong, I'm just explaining its thought process)