The alternatives like ASM.js and PNACL are far from usable. ASM.js has no support for threads and PNACL is unlikely to be supported outside of Chrome. They also have no debugging support.
Also 10 years ago Java was nowhere near as fast as it is now. If you are saying that Javascript might be an option 10 years from now, I am not disagreeing with you.
Your demo was also choppy for me on 2.2 Core 2, 460m, Chrome 29, Win7.
After your experience with both native and WebGL game development, don't you think it's a little premature to make a hardcore game targeting only WebGL?
As a hardcore SC2 player, I'd only be interested in a native version of this game. Even the latest ASM.JS demos like Epic Citadel run chopping on my system. Hardcore gamers like myself won't sacrifice performance for a the luxury using poorly designed and immature technology like JS and WebGL.
And Epic's demo was their previous gen engine, Unreal Engine 3, which targets mobile platforms: iOS, Android, PSP...
Meanwhile, the state of the art UE4 is only aimed at next gen consoles and native PCs games.
When emscripten is passed the debug flag, it will generate source maps, which will let you step through your code, although inspecting variables still isn't a solved problem.
If you look at this HTML5/WebGL minecraft engine, it stutters even without any other players or bots in the environment.
http://voxeljs.com/#gallery
Meanwhile Minecraft running in Java is smooth on even the slowest machines.
Benchmarks indicate that Javascript is 4x slower than Java.
http://j15r.com/blog/2013/07/05/Box2d_Addendum
The alternatives like ASM.js and PNACL are far from usable. ASM.js has no support for threads and PNACL is unlikely to be supported outside of Chrome. They also have no debugging support.