I think you are underestimating the amount of time and effort to create (i.e. rewrite the entire engine) with a native exporter. As Ashley has previously stated, by the time the new engine is finished, mobile processors will be running javascript quick enough for more advanced games.
I think a BIG advantage in writing plugins/behaviours with javascript is that functionality can be developed alot quicker than a compatible exporter could be.
Perhaps a middle ground might be to include more asm.js code (we already have box 2d with asm.js). But writing and maintain both versions would slow development down to a snails pace.
Unity and other options exist to create native apps. C2 is easier to use, but thats the trade off for mobile develop (at the moment).