I'm really surprised this isn't a sticky. This is by far the most important thread about HD video from the 5D Mark II.
I've found that with the settings tweaked as suggested there is some weird texture-like effect on some stuff. You can see it particularly easily on oof specular highlights because they're so smooth.
I still have to resize the video for editing, but that's ok because you can swap the original in to where the resized one was for exporting full size.