VLC does use VA-API on linux, though. I guess the rationale is that people with high-end AMD and nVidia GPUs are likely to have plenty of CPU horsepower, and acceleration is mostly needed for people with those intel IGPs that VA-API supports.
(EDIT: the real reason VA-API is used over VDPAU or XvBA is probably pragmatic and related to driver stability)
After having a look at VA-API vs VDPAU, I must say VDPAU is much nicer. VDPAU allows you to define times when frames will be shown, so vsync is handled fully in hardware; more than one transparent sub-picture can also be shown at one time.
(EDIT: the real reason VA-API is used over VDPAU or XvBA is probably pragmatic and related to driver stability)