Honestly, I think the main reason is inertia. Some of our customers started using VP6 back in 2007-2008, and don't want to simultaneously support two codecs. They generally want to switch down the road, but it will take a bit of work to re-encode their backlog.
Licensing is the other issue: VP6 is royalty-free, while H.264 isn't.
Lots of the Intel cards are low bar OEM, have little video memory and only really support fixed function pipelines rather than shader models. So you can't make stuff look as good and the bottom end of the market dictates how much stuff you can do 'mainstream'. Meaning lots of cards can't handle shaders which improve rendering quality immensely and put it on the GPU.