It's mostly because these apps run the sites through a remote server, which translate them for the iPad and then send them to you. As you can image it takes a lot of server power to do this, and the moment one of these apps becomes popular it starts to degrade.
So, they typically get some good reviews, then almost immediately become too slow to for good video; after a few thousand people start using them.
There is no fix, except to find video sites that have had the foresight to update. Since Adobe recently updated their server software to automatically detect mobile devices and server HTML 5 video, there is less and less excuses for sites to not support HTML 5. And with Adobe announcing that they will no longer be developing Flash for mobile devices, the pressure to update just went up two or three notches.
In the mean time, it is what it is.