You still get all the hardware acceleration via wrappers like WebGL, popular libs use instruction sets that map nicely to low-level concepts (simd for physics, etc.) and so on. HTML5 (html/css/js + wrapper + apis + libs) is not responsible for bad performance.
Native and platform specific optimisations always come last in terms of cost/benefit ratio ; there's usually a lot to be gained from higher level optimisations first (resource management, entity lifecycles, naive algorithms and sub-optimal logic, etc.)
So I'm not too sure what the problem is If you're targeting only one specific platform and want the absolute best performance (at the cost of iteration time, design time, prototyping time, etc.) why bother with high-level tools at all, and why not go low level in the first place ?