People who want bytecode has nothing to do with bytecode being better; they want bytecode because they want their language of choice to be a first class citizen and JavaScript-as-assembly means their language will always be second class.
I've never seen a bytecode that wasn't just a straightforward source-to-source translation of some language. JVM bytecode is pretty much just another way to encode Java (invokedynamic notwithstanding). .NET bytecode is pretty much just another way to write C#.
Bytecode really is nothing more than just a compressed source encoding of some language. It doesn't magically result in a VM that can efficiently encode all semantics of all programming languages, and I don't believe such a VM can exist anyway.
Not sure about the JVM, but .NET compiles to an intermediate language called CIL before creating the bytecode. I agree with you, but to bytecode advocates, this is an emotional issue. They do not want JavaScript to be the first-class language and their pet language to be "held back" by it.
That's similar to saying that x86 asm is able to deal with a large number of paradigms. LLVM IR might be a a viable target to avoid writing your own native code generators, but that does not a universal bytecode VM for dynamic languages make.
It sure would have been nice if Parrot had succeeded there...
Languages targeting bytcode platforms are just as liable to be second-class citizens as ones targeting JavaScript.
Scala and Clojure don't support proper tail calls. Why? Because the JVM is the Java Virtual Machine! I believe there were similar issue for dynamic languages on the JVM for the longest time as well.
And now just imagine implementing a Haskell->JVM compiler. I wouldn't be surprised if that's actually more difficult than implementing a Haskell->JavaScript compiler.
So yes: with JavaScript as the target, other languages are second-class citizens. But with some bytecode, that won't probably won't change much. Knowing how these things get designed, the end result could easily be that every language including JavaScript becomes a second-class citizen.