I think the problem with Java applets and Flash was not the bytecode but the slow startup (Java) and the closed source software (Flash) as well as the poor integration with HTML. There is no reason why browsers couldn't implement the same functionality we have now with Javascript using a bytecode based VM.
It just isn't standardized, or made available to website authors directly (there would likely need to be significant extra security audits before you could contemplate something like that...).
Since you would need backwards compatability, just make an argument to script elementa that specify the byte code to use instead of the javascript. Then older browsers could continue to function and the rest of us don't have to wait.
