JIT-Support is listed as a possible future feature for WASM: http://webassembly.org/docs/future-features/. Why shouldn't a WASM program not be able to generate WASM bytecode at runtime? The runtime-generated bytecode can be verified and then compiled by the WASM compiler, just like it is done for AOT-generated WASM bytecode. That said, I am not sure if WASM should support jitting. But if there is demand for it, then it will probably get done.

What I would really like to see is GC support in WASM. That would make it possible to AOT-compile managed languages like C#/Java to WASM. You wouldn't need to port the whole VM, "just" translate e.g. *.class-files to WASM which would seem a lot more feasible for the moment. That would sure only allow a subset of C#/Java, but since the web environment is distinct enough and the subset is large enough that would IMHO be acceptable.