The probable reason is that the Flash plugin cannot take advantage of any kind of hardware acceleration supported by your graphics card driver. Everything is then decoded using the CPU.
The Intel drivers present in your system allow VLC to use your GPU instead of your CPU to render the movie with video acceleration which is much better for obvious reasons.
Also, Flash hardware acceleration API (Stage Video) requires developers to actually add support for it into their video player SWFs.
If the video player does not have built in support for it even if the version of Flash you have does have VA enabled and your drivers support it (seems they do since VLC is apparently using it) your video will be decoded via the CPU.