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).