Comment 11 for bug 968489

You can also disable hardware acceleration in Settings (right-click on YouTube video, third item from the bottom of the menu) – http://www.macromedia.com/support/documentation/en/flashplayer/help/help01.html
So you can keep vdpau for real video players.

This, however, has one fatal flaw: the Settings dialog in Flash Player doesn't respond to clicks under Compiz (and therefore standard Unity). So to uncheck that checkbox, you'll have to temporarily switch to Unity2d or another non-composite environment.

Adding "EnableLinuxHWVideoDecode=false" to /etc/adobe/mms.cfg looked promising too, but it doesn't have any effect with the current Flash Player.