I'm the quintessential example of someone who just doesn't care about 3D desktop effects. I've even spent two and a half years working for a GPU startup 10 years ago, and I totally agree with the premise that the GPU should be running the desktop. But until it's 100% rock solid, I truly don't care. I'm here with my 7 virtual desktops hotkey switched with ctrl+up and cntrl+down, and can't imagine why anyone would seriously prefer the added animation delay of watching a cube rotate. Of course, that is just me the esoteric linux using engineer.
I just checked wikipedia which answered my confusion reading the article. I.e. that beryl was part of the merge, and that there doesn't appear to be an alternative... except android. It seems like it will take an OS that needs to fit on a cell phone, to truly dictate that things like zooming windows are absolute requirements. So I think once we see the same OS being used on our cell phones as our workstations, is the day when the motivation will be in place to have a rock solid 3D desktop implementation.