This is the point I think the author and a lot of people are missing. It's not always about what is the best possible design, instead it is often "what we will get". Politics, ideology, and timing can often come in the way of "the best design".
I would love to use NaCl (I was cheering for it up until recently), but if only Chrome is implementing it then it's about as useful as a screwdriver that doesn't fit any screws.
asm.js is already a stronger candidate because I can use it right now and it will work everywhere. Obviously the browser vendors has to create asm.js specific optimizations for it to be truly great, but that is like fuzzing over the handle, grip and material of the screwdriver. It fits the screws, it gets the job done, it actually works.
What does it matter how great your technology is if it doesn't work? What does it matter if NaCl is ten times faster if I can't actually use it? From what I see, Mozilla isn't very hot on the idea of adopting NaCl, and Microsoft will probably not even touch it in this millennia.
If a client wants me to produce something, I can't use NaCl, because it won't actually run in non-chrome browsers (without installing plugins).
To me it appears that the choice is either asm.js or nothing. NaCl just isn't happening.