A big advantage of asm.js over PNaCl is that it's not LLVM.
On the other hand PNaCl is very tightly coupled to LLVM. Any time I find myself checking if a some $feature is available in PNaCl, the discussion revolves around what LLVM can or can't do and how LLVM does it, see [1] for most recent example.
I just can't see how PNaCl could be meaningfully reimplemented. Reimplementing it from scratch would require implementing something bug-for-bug compatible with LLVM. That's a gargantuan task. On the other end of the spectrum, why not just use the original implementation? Then it would work very much like any other plugin. I don't think it's a good solution. It seems the only remaining option is implementing it on top of LLVM. But then you still share all potential limitations (e.g. in portability) and all security issues with all other LLVM-based implementations. It could end up being not that bad -- it means more work on LLVM itself, making it better -- but I'm not sure if that would offset the other problems. How many features that appeared first in chrome or webkit were then reimplemented elsewhere in a different, better way? Do we want to end up with only one browser? No, there are lots of things we wouldn't have if Firefox didn't happen, there are lots of things we wouldn't have if Chrome didn't happen. Do we want to end up with only one PNaCl runtime?
[1]: https://code.google.com/p/nativeclient/issues/detail?id=3475