JS does not cut it
The java fanbois have been claiming the same for years: "Java is within 50 % of C/C++ performance".This is true if you confuse a certain benchmark with *real* applications.
But everything non-trivial like a 3D action game, a CAD package or an image editing program simply needs C or C++ to deliver complex features with acceptable response time. And that is exactly because the memory structures and allocation/deallocation patterns must be customized to the problem at hand. There are lots of applications where memory is still at a premium, so compact storage is critical. Think of an engineer "flying" through the mechanical design of an Airbus A380. This is still a huge computer science challenge if every part can be manipulated/inspected/filtered individually. Or a multi-billion transistor chip design flow.
Also, the argument of architecture-neutrality does not stick. All platforms which have gcc and NPAPI can run Native Applets, as long as only c or c++ is used. Developers don't even need to cross-compile themselves; this could be done by entities like Google, the Mozilla foundation or GNU.
In case the compiler is supposed to implement security assurances (not the case with the current native client implementation), the object code could be digitally signed by a Trusted Compilation Provider (similar to a Certificate Authority)
Native Client, Google Chrome, Linux Security Modules and BSD Jails are innovative concepts which deserve more investment. The current state of application delivery and installation is very 1980ish, so to speak.