The quality of the NaCl work is not the problem.
The problem is that none of the other browser vendors can or will afford to get on Google's treadmill, trust Google as much as they would have to, then try to implement Pepper (for which the code is the spec, including bug for bug compat), take on all the toolchain dependencies, and hire people to co-maintain on their own release schedules. Not gonna happen.
The OS-specific toolchain-and-runtime alternative looks likelier to me. It solves the distribution problem, sinks the costs at the OS vendors, and avoids requiring coordination at the price of the safe plugins still being OS-specific binaries (which we live with today).
Another problem I have with your comment is the hope that innovation speeds up when we have more native-code plugin options. I doubt that greatly.
Web developers can choose different tools today, but their complexity is mostly confined to the server side and to the development lifecycle there.
Moving some or all of this complexity to the browsers via a large and growing menu of "DLLs" that are required to be downloaded along with primary app source? No way. Remember, the whole gambit of NaCl requires the humongous and messy Pepper API, the API that is nowhere near standardized or ready (or able) to be standardized, which non-chromium.org browsers are not going to support.
It's like the >1000 MS-COM interfaces that ActiveX plugins can and do use in old IE versions.
My bet is that the client side will not grow to look like your random Apache installation with (magically memory- and control-flow-safe) multiple programming language DLLs lying about. We may get to a post-JS future but it won't be that Tower of Babel, not on the client -- especially not on the mobile client.