The toolchain is better for embedding existing native applications in the browser with PNaCl. There's a lot of code out there which isn't written in JavaScript, and it would be nice to apply the same sandboxing guarantees. Again, it's not that you can't compile C to asm.js (yeah, emscripten does work), but I think the PNaCl toolchain is just better.
I'd prefer to think that most efficient rather than most advanced tools win. look at hammer, axe, knife, nail. they are pure utility expressed as output divided by complexity of use
