The interaction between C and Javascript offered by Emscripten is a lot better than JNI on Android. I wish the Android NDK would steal a few ideas from Emscripten, but all the Android teams at Google don't seem to be able to look outside the nice comfy bubble they've created for themselves.
With Emscripten, you can embed Javascript source code directly into the C code and then call the embedded JS function from the C side as well as C functions from inside Javascript.
In my case I usually debug the platform-agnostic code compiled natively in IDEs like Visual Studio or Xcode, and for the HTML5 specific code (which is just a few hundred lines) traditional "printf-debugging".
How about debugging? Is it possible to step through a mix of C and JS stack frames?