The W3C and WHATWG are mainly just forums. They have some policies that may help or hurt standards work a little bit, but most responsibility for the state of Web standards rests on the participants in standards groups, especially browser vendors, who drive the development of most Web standards and are responsible for implementing most of them too. Therefore, most of the blame for problems in Web standards should be assigned to the specific browser vendors who generated and implemented those standards, and influenced them in various directions.
For example, the reason media element playback, Web Audio and MediaStreams are all quite different APIs is because when I proposed a MediaStream-based alternative to Web Audio, no other browser vendors were interested. Google already had separate teams working on Web Audio and MediaStreams and was already shipping behind a prefix, Apple was barely engaged at all in the Web Audio working group, and Microsoft was completely disengaged. It's not because of anything specifically wrong with the W3C or WHATWG. (FWIW I'm not saying my proposal was necessarily better than what we got; there are technical reasons why it's hard to unify these APIs.)
In fact, even assigning responsibility to individual browser vendors glosses over important distinctions. For example, even within the Chrome team you've got teams who care a lot about Web standards and teams who care a bit less.
One way to make positive change for Web standards is to single out specific undesirable behavior by specific vendors and call them out on it. I know (from both giving and receiving :-) ) that that has an impact. Assigning blame more generally is less likely to have impact.