In the long run, yes, it's pretty much the same as JIT-ed Java. But technology always seems to be a moving target, and native, compiled binaries are probably going to be important for a long time.
The interesting thing is that now the plugin developer controls the system call interface, not the OS. They could develop a suitable layer of abstraction for a lot of things that you'd ordinarily need an OS for, and would go out of your mind to port.
The applet sandbox was in the same position. The limitation has been security and compatibility. As the applet sandbox has been extended (for instance, with QT4J), both security and compatibility have become problems. I don't see how NaCL avoids those.
The interesting thing is that now the plugin developer controls the system call interface, not the OS. They could develop a suitable layer of abstraction for a lot of things that you'd ordinarily need an OS for, and would go out of your mind to port.