This maybe a known trick because its so simple. But if you don't mind low quality video playback but smooth playback, try this.
Adjust your compatibility options for Hulu Desktop to open it with
Disable visual themes
Disable desktop composition
Run in 640x480 screen resolution
This will make the menus a bit blurry but the video still looks good enough to me to watch. This isn't a permanent fix as we are all still waiting for hardware acceleration in flash.
Edit: Make sure to turn down quality in Hulu to medium or low*
*Depending on the video being watched