First, hardware (i.e. GPU) acceleration makes a significant difference only when decoding h.264. For h.263 and On2 V6 you shouldn't need hardware acceleration. GPU accelerated h.264 came in Quicktime X in Snow Leopard and is not available on all Snow Leopard compatible machines. The disparity in performance between Quicktime, and other player-codec packages for that matter, and Flash has been around for years.
The second, and more important in my opinion, reason is that Flash doesn't have performance and stability issues only when it comes to video. They are more apparent with video, but all kinds of content - games, sites, even sometimes ads - make the Flash plugin disproportionately task the system.