If everyone moves to iPads and iPhones, no amount of Emscripten will address the problem that the browser doesn't have access to the actual hardware. No talking to bluetooth devices, no talking to the GPU, no ad-hoc wifi communication with other devices, etc.

Mozilla and Google have been pushing on exposing more features like that to the web browser, but that's something Apple seems uninterested in (because it diminishes the importance of their App Store)