Nice idea but windowless flash are also more cpu consuming, so ads would use more cpu. I wonder what's the environmental impact of a change like this would be ;)
What's strange was that performance was my original thought when seeing that title, flash is breaking the web is so many ways.
I'm not sure it would change anything for Chrome though, the plugin in a process seems to use the windowless model by default. I'm not sure about that, but the rendering speed while doing my experimentations with http://swiffout.com seemed to suggest that.