My comments aren't about GUIs. A command-line interface is still a user interface. It still needs to be designed for the user experience. I count developers as a type of user, and just as much care should to be put into the discoverability, accessibility, and usability in the software that developers must use as is put into the software that end users must use.
On the command line I don't see it as an issue. Both emscripten and NaCl provide standard gcc-style cross-compiling toolchains that are easy to integrate with other higher level build systems. That's IMHO the only way that makes sense when providing a C/C++ compiler toolchain. The big missing piece in the puzzle is interactive debugging, hopefully with WebAssembly we also get proper debug information format (something better then source-maps), and can then debug-step in the browser through the original source code (this sort-of already works with emscripten since it can generate source maps, but it is quite rough for big scripts, and mapping back variable names doesn't work very well).
