One of the big issues with NaCl is that the API it used wasn't standardized at all and there was only a single implementation. You could pick a random function and ask "hey, what happens if you pass in some slightly weird arguments?" and there was no answer beyond "whatever Chrome does". With enough work, maybe that could have been overcome while preserving backwards compatibility, but there were lots of random functions in there because somebody or other had found it useful. WASM was built from the ground up with a standards process and multiple implementations.