Often things win not through fair competition. For example, WebSQL "won" on mobile because WebKit won on mobile, and WebKit happened to have WebSQL. If WebKit had had, say, the Audio Data API (which it did not), then the Audio Data API would have "won". Neither of those APIs won or would have won on its own merits, but because it was backed by the 800 pound gorilla in the space. (I chose Audio Data as an example because it is not in the same space as WebSQL, i.e. not competing with it, and was a nice API, that failed).
And the problem is that PNaCl will fragment the web, and already has. That's a serious problem - for everyone but Google.