VLC is more then a UI, they have to implement the decoders in libavcodec, and they do a lot of work to package things underneath. FFmpeg also supports VDPAU (the nvidia, linux video acceleration api), but it would still be some work for VLC to implement it.
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.
