It seems like anything you can do with bytecode you can do just as easily and much faster in native code. In theory, you could even retain platform and language independence by distributing programs and libraries in bytecode then compiling to native code at installation, rather than JITing it.
So in general, when would you want to execute bytecode instead of native?
I think you just answered your own question: platform independence. Platform-independent bytecode is produced and distributed to its target platform. When executed it's quickly compiled to native code either before execution begins, or simultaneously (Just In Time). The Java JVM and presumably the .NET runtimes operate on this principle.
All good answers, but my hot-button has been hit - performance.
If the code being run spends all its time calling library/system routines - file operations, database operations, sending windows messages, then it doesn't matter very much if it's JITted, because most of the clock time is spent waiting for those lower-level operations to complete.
However, if the code contains things we usually call "algorithms", that have to be fast and don't spend much time calling functions, and if those are used often enough to be a performance problem, then JIT is very important.
Hank Shiffman from SGI said (a long time ago, but it's till true):
So when considering byte code vs native, consider which trade-offs you want to make between portability, security, size, and execution speed. If speed is the only important factor, go native. If any of the others are more important, go with bytecode.
I'll also add that maintaining a series of OS and architecture-targeted compilations of the same code base for every release can become very tedious. It's a huge win to use the same Java bytecode on multiple platforms and have it "just work."
Bytecode creates an extra level of indirection.
The advantages of this extra level of indirection are:
Some of the disadvantages:
Ideally you would have portable bytecode that compiles Just In Time to native code. I think the reason bytecode interpreters exist without JIT is due primarily to the practical fact that native code compilation adds complexity to a virtual machine. It takes time to build, debug, and maintain that additional component. Not everyone has the time or resources to make that commitment.
A secondary factor is safety. It's much easier to verify an interpreter won't crash than to guarantee the same for native code.
Third is performance. It can often take more time to generate machine code than to interpret bytecode for small pieces of code that only run once.
The performance of essentially any program will improve if it is compiled, executed with profiling, and the results fed back into the compiler for a second pass. The code paths which are actually used will be more aggressively optimized, loops unrolled to exactly the right degree, and the hot instruction paths arranged to maximize I$ hits.
All good stuff, yet it is almost never done because it is annoying to go through so many steps to build a binary.
This is the advantage of running the bytecode for a while before compiling it to native code: profiling information is automatically available. The result after Just-In-Time compilation is highly optimized native code for the specific data the program is processing.
Being able to run the bytecode also enables more aggressive native optimization than a static compiler could safely use. For example if one of the arguments to a function is noted to always be NULL, all handling for that argument can simply be omitted from the native code. There will be a brief validity check of the arguments in the function prologue, if that argument is not NULL the VM aborts back to the bytecode and starts profiling again.